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PubMed1981

Epstein-Barr virus DNA. X. Direct repeat within the internal direct repeat of Epstein-Barr virus DNA.

The 3,360-base-pair internal direct repeat (IR) in Epstein-Barr virus DNA separates the short and long unique DNA domains. IR has a single BamHI site. The juncture between the short unique domain and IR has been mapped by restriction endonucleases and is less than 2,600 nucleotides before the BamHI site in IR. The junction between IR and the long unique domain has been sequenced and is approximately 650 nucleotides after the BamHI site in IR. Thus, relative to the start of IR at the juncture with the short unique domain, the last repeat is at least 90 base pairs short of being complete. There is homology between the 250-nucleotide fragments to the left and the right of the unique BamHI site in IR. A 35-base-pair sequence of the left fragment is directly repeated within the right fragment, once fully and once partially. The implications of these findings are discussed.

DNA Restriction Enzymes↗
PubMed1997

A new class of defective hepatitis B virus genomes with an internal poly(dA) sequence.

Sequence heterogeneity of hepatitis B virus (HBV) is increasingly recognized to play a role in virus-host interaction. We have used a recently established method for HBV full-length genome amplification to search for novel types of HBV variants and to investigate further the sequence heterogeneity of HBV genome populations. Using this method, a substantial fraction of HBV genomes much shorter than wildtype size was found in some sera and liver biopsies from infected patients. Cloning and sequencing of a number of these HBV genomes as well as hybridization studies revealed a new minor class of HBV genomes with an internal poly(dA) sequence approximately 60 to more than 100 nucleotides long in 4 of 10 patients. The 5'-ends of the internal poly(dA) sequences are located at positions corresponding to the authentic processing/polyadenylation sites of the RNA pregenome, whereas the positions of the 3'-ends are variable due to different sizes of adjacent deletions. These data suggest that the poly(A) tail of the pregenomic RNA is occasionally reverse transcribed by the HBV P-protein and during this process a deletion seems to be introduced into the DNA minus strand. We propose a mechanism by which this could be accomplished during DNA minus strand synthesis.

Base Sequence↗
PubMed2005

Human immunodeficiency virus Nef induces rapid internalization of the T-cell coreceptor CD8alphabeta.

Human immunodeficiency virus (HIV) Nef is a membrane-associated protein decreasing surface expression of CD4, CD28, and major histocompatibility complex class I on infected cells. We report that Nef strongly down-modulates surface expression of the beta-chain of the CD8alphabeta receptor by accelerated endocytosis, while CD8 alpha-chain expression is less affected. By mutational analysis of the cytoplasmic tail of the CD8 beta-chain, an FMK amino acid motif was shown to be critical for Nef-induced endocytosis. Although independent of CD4, endocytosis of the CD8 beta-chain was abrogated by the same mutations in Nef that affect CD4 down-regulation, suggesting common molecular interactions. The ability to down-regulate the human CD8 beta-chain was conserved in HIV-1, HIV-2, and simian immunodeficiency virus SIVmac239 Nef and required an intact AP-2 complex. The Nef-mediated internalization of receptors, such as CD4, major histocompatibility complex class I, CD28, and CD8alphabeta, may contribute to the subversion of the host immune system and progression towards AIDS.

Alleles↗
PubMed2004

La protein binding at the GCAC site near the initiator AUG facilitates the ribosomal assembly on the hepatitis C virus RNA to influence internal ribosome entry site-mediated translation.

Human La autoantigen has been shown to influence internal initiation of translation of hepatitis C virus (HCV) RNA. Previously, we have demonstrated that, among the three RRMs of La protein, the RRM2 interacts with HCV internal ribosome entry site (IRES) around the GCAC motif near the initiator AUG present in the stem region of stem-loop IV (SL IV) (Pudi, R., Abhiman, S., Srinivasan, N., and Das S. (2003) J. Biol. Chem. 278, 12231-12240). Here, we have demonstrated that the mutations in the GCAC motif, which altered the binding to RRM2, had drastic effect on HCV IRES-mediated translation, both in vitro and in vivo. The results indicated that the primary sequence of the stem region of SL IV plays an important role in mediating internal initiation. Furthermore, we have shown that the mutations also altered the ability to bind to ribosomal protein S5 (p25), through which 40 S ribosomal subunit is known to contact the HCV IRES RNA. Interestingly, binding of La protein to SL IV region induced significant changes in the circular dichroism spectra of the HCV RNA indicating conformational alterations that might assist correct positioning of the initiation complex. Finally, the ribosome assembly analysis using sucrose gradient centrifugation implied that the mutations within SL IV of HCV IRES impair the formation of functional ribosomal complexes. These observations strongly support the hypothesis that La protein binding near the initiator AUG facilitates the interactions with ribosomal protein S5 and 48 S ribosomal assembly and influences the formation of functional initiation complex on the HCV IRES RNA to mediate efficient internal initiation of translation.

Amino Acid Motifs↗
PubMed1998

Deletion of internal sequences results in tobacco mosaic virus defective RNAs that accumulate to high levels without interfering with replication of the helper virus.

Deletion of certain internal sequences of the tobacco mosaic tobamovirus (TMV) genome was required to create replication-defective RNAs (dRNA) that were replicated in trans by TMV. All dRNAs that accumulated to detectable levels were missing nucleotides 3420-4902, which appeared to constitute a core region that inhibited replication in trans. Deletion of additional sequences resulted in dRNAs that varied tremendously in ability to be replicated from none to levels exceeding that of the helper viral RNA. Accumulation of dRNA negative- and positive-stranded RNAs of each dRNA paralleled those of the helper virus. Negative-stranded RNA accumulation of both helper and dRNA ceased at the same early time in the infection while synthesis of both positive-stranded RNAs continued, suggesting that both dRNAs and helper virus RNAs were synthesized from the same pool of replicase complexes. Positive- to negative-stranded RNA ratios for the dRNAs were similar to, or slightly greater than the wild-type helper virus. Full-length dRNAs were not supported in trans by a replication-competent helper virus. Even though some of the artificially constructed dRNAs accumulated to levels exceeding the level of the helper virus, none appreciably affected the replication of the helper virus, suggesting that the dRNAs are produced from "excess" replicase capacity.

DNA-Directed DNA Polymerase↗
PubMed1995

Protein and virus crystal growth on international microgravity laboratory-2.

Two T = 1 and one T = 3 plant viruses, along with a protein, were crystallized in microgravity during the International Microgravity Laboratory-2 (IML-2) mission in July of 1994. The method used was liquid-liquid diffusion in the European Space Agency's Advanced Protein Crystallization Facility (APCF). Distinctive alterations in the habits of Turnip Yellow Mosaic Virus (TYMV) crystals and hexagonal canavalin crystals were observed. Crystals of cubic Satellite Tobacco Mosaic Virus (STMV) more than 30 times the volume of crystals grown in the laboratory were produced in microgravity. X-ray diffraction analysis demonstrated that both crystal forms of canavalin and the cubic STMV crystals diffracted to significantly higher resolution and had superior diffraction properties as judged by relative Wilson plots. It is postulated that the establishment of quasi-stable depletion zones around crystals growing in microgravity are responsible for self-regulated and more ordered growth.

Crystallization↗
PubMed1985

Role of cell membrane composition in receptor-mediated internalization of vesicular stomatitis virus in human HEp-2 cells.

The role of essential fatty acids in membrane functions related to receptor-mediated endocytosis of vesicular stomatitis virus (VSV) was investigated using a human laryngeal carcinoma cell line (HEp-2) grown in chemically defined serum-free medium (DM) to deplete their essential fatty acid contents. VSV replicated much less effectively in HEp-2 cells grown in DM as compared to serum containing complete medium (CM). Observed reduction in the rate of virus multiplication was, at least in part, due to reduced virus penetration which was monitored using VSV labeled with nitroxyl free radicals as electron spin probe. Surface proteins of VSV were labeled with maleimide spin-label, and succinimide spin-label. Ni2+ was used as a broadening agent to identify the spin-label signals from viruses inside the cell. HEp-2 cells and mouse leukemia cell line L1210 treated with 5-dimethylaminonaphthalene-1-sulfonyl (dansyl) cadaverine, an agent previously shown to inhibit the uptake of VSV in vitro, was used as a positive control in some experiments. VSV penetrated less effectively in both DM-grown cells and in CM-grown cells in the presence of dansylcadaverine. Similar results were obtained by monitoring the uptake of 125I-labeled VSV. When HEp-2 cells grown for several generations in DM were incubated with 10% fetal calf serum for 16 h, the cells supported virus replication to a similar extent as the cells grown in CM. In contrast, addition of arachidonic acid restored VSV growth only partially. Continued growth of HEp-2 cells in DM resulted in a shift in fatty acyl chain composition of phospholipids. The results indicate a finite role for essential fatty acids in receptor-mediated internalization of virus particles.

Animals↗
PubMed1995

Alternative translation initiation of the Moloney murine leukemia virus mRNA controlled by internal ribosome entry involving the p57/PTB splicing factor.

Moloney murine leukemia virus (Mo-MuLV) genomic mRNA codes for two gag precursors by alternative initiations of translation. An AUG codon governs the synthesis of the retroviral capsid proteins precursor, whereas a CUG codon directs the synthesis of a glycosylated cell surface antigen, the gross cell surface antigen. Control of the relative synthesis of the two precursors is crucial for MuLV infectivity and pathology. Furthermore, the MuLV mRNA leader sequence is very long and should inhibit translation according to the classical scanning model. This suggests a different translation initiation mechanism allowing gag efficient expression. We demonstrate, by using bicistronic vectors expressed in COS-7 cells, that the Mo-MuLV mRNA leader drives translation initiation by internal ribosome entry. We have localized the internal ribosome entry site (IRES) between the two initiation codons. This 126 nucleotide long IRES implies an oligopyrimidine tract located 45 nucleotides upstream of AUG codon. UV cross-linking and affinity chromatography experiments show that the PTB/p57 splicing factor specifically interacts with this oligopyrimidine tract. The MuLV IRES controls alternative translation initiation by activating the capsid protein precursor expression. This gag translational enhancer could exist in other retroviruses.

Animals↗
PubMed1999

RNA replication for the paramyxovirus simian virus 5 requires an internal repeated (CGNNNN) sequence motif.

A functional RNA replication promoter for the paramyxovirus simian virus 5 (SV5) requires two essential and discontinuous elements: 19 bases at the 3' terminus (conserved region I) and an 18-base internal region (conserved region II [CRII]) that is contained within the coding region of the L protein gene. A reverse-genetics system was used to determine the sequence requirements for the internal CRII element to function in RNA replication. A series of copyback defective interfering (DI) RNA analogs were constructed to contain point mutations in the 18 nucleotides composing CRII, and their relative replication levels were analyzed. The results indicated that SV5 DI RNA replication was reduced by substitutions for two CG dinucleotides, which in the nucleocapsid template are in the first two positions of the first two hexamers of CRII nucleotides. Substitutions for other bases within CRII did not reduce RNA synthesis. Thus, two consecutive 5'-CGNNNN-3' hexamers form an important sequence in the SV5 CRII promoter element. The position of the CG dinucleotide within the SV5 leader and antitrailer promoters was highly conserved among other members of the Rubulavirus genus, but this motif differed significantly in both sequence and position from that previously identified for Sendai virus. The possible roles of the CRII internal promoter element in paramyxovirus RNA replication are discussed.

Promoter Regions, Genetic↗
PubMed1990

[Effects of remantadine on fusion of lipid membranes of influenza A virus with plasma and internal membranes of lymphoblastic cells].

The method of fluorescence dequenching was used to study the interaction between influenza virus A/Krasnodar/101/59 and Namalwa and Raji lymphoblastoid cells. Experiments with endocytosis inhibitors and fluorescence quenchers have shown that at pH = 5.0 the virus lipid envelopes are fused with the plasma membranes of the cells, and at pH = 7.4 the virus lipid envelopes are fused with the internal, presumably endosomal, membranes of the cells. Remantadine at a concentration of 50-1000 micrograms/ml did not influence the fusion of virus lipid envelopes with intracellular membranes at pH = 7.4 whereas at pH = 5.0 it inhibited, beginning from 25 micrograms/ml concentration, the fusion of virus lipid envelopes with the plasma membranes of cells.

Adamantane↗
PubMed1989

An international collaborative study of an anti-infectious bursal disease virus reference serum.

Fourteen laboratories participated in a collaborative study of a freeze-dried preparation of anti-infectious bursal disease virus serum to assess the suitability of the serum as a standard for use in the infectious bursal disease virus neutralization test. Ten laboratories carried out micro-virus neutralization tests and six carried out plaque reduction tests, two laboratories carrying out both tests. When titres were expressed as a proportion of that obtained for a reference preparation there was a marked reduction in variation between results from different laboratories. The use of a reference preparation was therefore of value when comparing results from different laboratories. It is proposed that the reference preparation used in this study be used as a standard to facilitate the comparison of results from different laboratories. The proposed standard contains by definition 10,000 UK units.

Animals↗
PubMed2002

Human papillomavirus virus-like particles do not activate Langerhans cells: a possible immune escape mechanism used by human papillomaviruses.

High-risk human papillomaviruses are linked to several malignancies including cervical cancer. Because human papillomavirus-infected women do not always mount protective antiviral immunity, we explored the interaction of human papillomavirus with Langerhans cells, which would be the first APCs the virus comes into contact with during infection. We determined that dendritic cells, normally targeted by vaccination procedures and Langerhans cells, normally targeted by the natural virus equally internalize human papillomavirus virus-like particles. However, in contrast to dendritic cells, Langerhans cells are not activated by human papillomavirus virus-like particles, illustrated by the lack of: up-regulating activation markers, secreting IL-12, stimulating T cells in an MLR, inducing human papillomavirus-specific immunity, and migrating from epidermal tissue. Langerhans cells, like dendritic cells, can display all of these characteristics when stimulated by proinflammatory agents. These data may define an intriguing immune escape mechanism used by human papillomavirus and form the basis for designing optimal vaccination strategies.

Animals↗
PubMed1982

Experimental infection of Norvegian rats (Rattus norvegicus) with ratpox virus.

Young as well as adult free living Norvegian rats (Rattus norvegicus) were highly susceptible to intranasal, intradermal and natural infections with the ratpox virus belonging to genus Orthopoxvirus. Disseminated disease occurred in infected rats due to generalization of the virus to internal organs. In survivors, virus was excreted for a longer period of time (more than 1 month) in faeces and urine.

Animals↗
PubMed2004

Effects of lipid rafts on dynamics of retroviral entry and trafficking: Quantitative analysis.

The association of cell surface receptors with sterol-sphingolipid-enriched microdomains of the plasma membrane, so-called lipid rafts, may affect the receptor-mediated entry and trafficking dynamics of viruses. A model retrovirus, subgroup A avian sarcoma and leukosis virus (ASLV-A), can initiate infection by binding to either of two forms of the tumor virus subgroup A (TVA) receptor, a lipid-raft-associated glycosylphosphatidylinositol (GPI)-anchored receptor (TVA800) or a transmembrane receptor (TVA950). Narayan et al. previously found that virus particles bound to TVA950 were more rapidly internalized than virions bound to TVA800, and the internalization via TVA950 exhibited biphasic kinetics. To explore potential molecular mechanisms for these results we developed a mathematical model that accounts for internalization of viruses through cellular pits, trafficking to an endosomal compartment where fusion occurs, and viral DNA synthesis. By fitting the model to experimental data we found that viruses bound to TVA950 were internalized up to 2.6-fold more rapidly than viruses bound to TVA800. Two- to threefold greater lateral diffusivities of transmembrane proteins, relative to GPI-anchored proteins, observed in other systems, suggest that the internalization rate of ASLV-A is diffusion-limited. Furthermore, by allowing for recycling of internalized TVA950-bound viruses back to the cell surface, we can account for the observed biphasic internalization kinetics. This mechanism is also consistent with the observed slower rate of DNA synthesis for viruses that enter via TVA950. Overall, the model provides a means to generate new experimentally testable hypotheses and sets a foundation for building a quantitative and integrated understanding of viral entry, trafficking, and intracellular dynamics.

Animals↗
PubMed1999

Quantitative detection of hepatitis B virus DNA in two international reference plasma preparations. Eurohep Pathobiology Group.

Quantitative detection of hepatitis B virus (HBV) in serum or plasma is of significance for monitoring of therapy and establishment of the prognosis of the disease, as well as for infectivity assessment and quality control of the diagnosis. Unfortunately, various commercially available test kits for HBV DNA yielded conflicting quantitative results, with differences of up to a factor of 120. The Eurohep Pathobiology Group has established two reference samples of plasma from HBV carriers and determined as accurately as possible the number of HBV DNA molecules in these samples. Plasma donations from two single highly viremic carriers of HBV genotype A (HBV surface antigen subtype adw2) and genotype D (ayw2/3), respectively, were collected, and coded dilutions of these samples were analyzed by members of the Eurohep Pathobiology Group. Quantitative results from the seven laboratories reporting consistent results were initially divergent. Limiting dilution and nested PCR assays suffered from incomplete DNA extraction. Hybridization assays used inaccurately quantitated cloned DNA as a reference. Two hybridization assays could not be calibrated directly with cloned HBV DNA, because virion-derived DNA reacted much less efficiently. After identification and elimination of these problems, limiting-dilution assays from three laboratories and hybridization assays from two producers generated consistent and concordant results: 2.7 x 10(9) HBV DNA molecules/ml (range, 2.1 x 10(9) to 3.4 x 10(9) HBV DNA molecules/ml) in the plasma from the carrier of genotype A and 2.6 x 10(9) HBV DNA molecules/ml (range, 2.1 x 10(9) to 3.0 x 10(9) HBV DNA molecules/ml in the plasma from the carrier of genotype D. The two Eurohep reference plasma samples have already been used for the standardization of test kits and in quality control trials, and the plasma from the carrier of genotype A will probably be the basis of a World Health Organization reference sample.

DNA, Viral↗