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At least 1,531 records · Page 85Linked to original sources
PubMed1996

Variation of viroid profiles in individual grapevine plants: novel grapevine yellow speckle viroid 1 mutants show alterations of hairpin I.

This is the first report which gives a general survey about viroid variant composition in a vineyard and within single plants. A German vineyard with 20-year-old grapevines (Vitis vinifera) of the cultivars 'Bacchus' and 'Kerner' was analysed for viroid infections. Only grapevine yellow speckle viroid 1 (GYSVd1) and the grapevine isolate of hop stunt viroid (HSVdg) were detected. Both viroids occur in several sequence variations. Eighteen novel GYSVd1 variants and two previously published HSVdg main variants with six new minor variants were found. They were randomly spread in the vineyard. The distribution of GYSVd1 and HSVdg main variants and their accompanying subvariants differed even in neighbouring plants. We conclude that these individual viroid variant profiles are the result of 20 years of independent evolution, i.e. mutation and selection, in each single plant. Four of the nine GYSVd1 main variants were mutated in the inverted repeats bordering the central conserved region. These base substitutions decreased the thermodynamic stability of a metastable structure called hairpin I.

Base Sequence↗
PubMed2004

Hepatitis C virus quasispecies variability modulates nonstructural protein 5A transcriptional activation, pointing to cellular compartmentalization of virus-host interactions.

Hepatitis C virus (HCV) behaves in infected patients as a complex mixture of genetically distinct but closely related variants referred to as a "quasispecies." By using quasispecies analysis strategies, we showed that HCV nonstructural protein 5A (NS5A) has a quasispecies distribution in infected humans and that NS5A quasispecies undergo significant genetic evolution over time, as a result of random accumulation of nucleotide mutations during replication. Genetic evolution of the NS5A quasispecies results in sporadic amino acid changes in the protein sequence. By using the functional in vitro model of HCV NS5A transcriptional activation in Saccharomyces cerevisiae, we showed that natural NS5A quasispecies variants induce different levels of transcriptional activation, according to the charge of the residues (and possibly minor conformational changes) in the quasispecies variant sequence. These findings show that the accumulation of mutations on HCV genomes during replication randomly generates variant proteins with quantitatively different functional properties. The fact that each new variant protein is initially produced in a single infected hepatocyte and may or may not subsequently spread throughout the liver (depending on the replication capacities of the variant virus) points to cellular compartmentalization of virus-host interactions during chronic infection. This feature of quasispecies-distributed viruses could play an important role in various aspects of the viral life cycle and related disease.

Amino Acid Sequence↗
PubMed1988

Expression of phosphoprotein p19 in brain, testis, and neuroendocrine tumor cells. Developmental regulation in rat brain.

We have recently purified from bovine brain a 19-kDa protein, p19, that was previously shown to undergo hormonally regulated phosphorylation in several neuroendocrine tumor cells. We now report the tissue distribution of p19, studied by immunoblotting. Using a rabbit antiserum, which binds both to the unphosphorylated form and to the two predominant phosphoforms of p19, we show that the protein is present in brain and testis but not in a variety of other mammalian tissues. High levels of p19 are also present in several cultured tumor cells expressing neuroendocrine properties. In addition, p19 was detected in HL60 promyelocytic leukemia and in Friend erythroleukemia cells, but not in several other cell lines. In rat brain, we show that the level of p19 is maximal on the first postnatal day and declines within the first 2 weeks of life to a low plateau that persists into adulthood. The concentration of translatable p19 mRNA also decreases postnatally in rat brain, suggesting that the developmental regulation of the expression of p19 occurs, at least in part, at a pretranslational level. The broad species cross-reactivity of the p19 antibody suggests that the gene encoding p19 has been highly conserved during mammalian evolution. Based on the pattern of expression of this protein, we propose that p19 plays a role in the development of neurons and neuroendocrine cell types.

Animals↗
PubMed2004

Analysis of HCV co-infection with occult hepatitis B virus in patients undergoing IFN therapy.

BACKGROUND/AIM: Occult hepatitis B virus (HBV) infection is characterized by the presence of HBV DNA in the absence of hepatitis B surface antigen (HBsAg) in the patient serum. Although such infections have been identified in patients with chronic hepatitis C, the clinical significance of those co-infections is still not understood. Our aim was, therefore, to assess the prevalence and clinical consequences of occult HBV infection in chronic hepatitis C patients undergoing antiviral therapy. METHODS: The study population consisted of 53 HBsAg-negative patients with chronic hepatitis C treated with IFN/ribavirin or IFN/ribavirin/amantadine. Nine patients experienced a viral breakthrough (BT), 30 were non-responders (NR) and 14 were responders (R). HBV-DNA detection by PCR was performed using primers specific for the S region of the HBV genome and HCV-RNA detection by PCR with primers localised in both the 5'NC and core region of HCV genome, before, during and after treatment. Viral genome sequences were also studied. RESULTS: Occult HBV genomes were found in the serum of four of 53 (7.5%) patients, unrelated to anti-HBc status. No significant differences in biochemical, virological, or histological markers, age, duration of infection, were observed in patients with or without HBV DNA. There was an inverse correlation in the evolution of HBV DNA and HCV RNA levels. Direct sequencing showed that S gene of occult HBV presented mutations in the "a" determinant while no specific mutation in the core region of HCV was observed. None of the four patients co-infected with HBV and HCV were responders to anti-HCV therapy. CONCLUSION: In our clinical setting, the prevalence of occult HBV co-infection among patients with chronic hepatitis C was low and independent of the presence of markers of previous HBV infection. Further studies in larger cohort of patients are warranted to determine if occult HBV co-infection may be involved in HCV resistance to combination therapy.

Adult↗
PubMed2001

The autocatalytic release of a putative RNA virus transcription factor from its polyprotein precursor involves two paralogous papain-like proteases that cleave the same peptide bond.

The largest replicative protein of coronaviruses is known as p195 in the avian infectious bronchitis virus (IBV) and p210 (p240) in the mouse hepatitis virus. It is autocatalytically released from the precursors pp1a and pp1ab by one zinc finger-containing papain-like protease (PLpro) in IBV and by two paralogous PLpros, PL1pro and PL2pro, in mouse hepatitis virus. The PLpro-containing proteins have been recently implicated in the control of coronavirus subgenomic mRNA synthesis (transcription). By using comparative sequence analysis, we now show that the respective proteins of all sequenced coronaviruses are flanked by two conserved PLpro cleavage sites and share a complex (multi)domain organization with PL1pro being inactivated in IBV. Based upon these predictions, the processing of the human coronavirus 229E p195/p210 N terminus was studied in detail. First, an 87-kDa protein (p87), which is derived from a pp1a/pp1ab region immediately upstream of p195/p210, was identified in human coronavirus 229E-infected cells. Second, in vitro synthesized proteins representing different parts of pp1a were autocatalytically processed at the predicted site. Surprisingly, both PL1pro and PL2pro cleaved between p87 and p195/p210. The PL1pro-mediated cleavage was slow and significantly suppressed by a non-proteolytic activity of PL2pro. In contrast, PL2pro, whose proteolytic activity and specificity were established in this study, cleaved the same site efficiently in the presence of the upstream domains. Third, a correlation was observed between the overlapping substrate specificities and the parallel evolution of PL1pro and PL2pro. Collectively, our results imply that the p195/p210 autoprocessing mechanisms may be conserved among coronaviruses to an extent not appreciated previously, with PL2pro playing a major role. A large subset of coronaviruses may employ two proteases to cleave the same site(s) and thus regulate the expression of the viral genome in a unique way.

Amino Acid Sequence↗
PubMed1998

Molecular inhibition of HIV type 1 by HIV type 2: effectiveness in peripheral blood mononuclear cells.

HIV-2 downregulates HIV-1 in human primary peripheral blood mononuclear cells (PBMCs). Although the effect of HIV-2 on HIV-1 in human CD4+ T cell lines was previously reported, the present observations with PBMCs are a necessary demonstration before considering animal model and clinical studies. Notably, the downregulation was observed with at least three phenotypically different HIV-1 proviruses and three different HIV-2 proviruses and was independent of the mode of introduction of the proviruses. HIV-2 inhibited both the production of extracellular HIV-1 p24 antigen and intracellular viral RNA, suggesting the involvement of transcriptional downmodulation. Some of the defective HIV-2 proviruses also inhibited HIV-1. In some cases, these defects were transcomplemented by the corresponding HIV-1 gene products, emphasizing cross-regulation between the two viruses. The phenotype of one of the mutant HIV-2 proviruses suggested that the posttranscriptional effects may also occur. In addition to the possible HIV-2 suppression of HIV-1 in vivo by cross-protective immune mechanisms, intracellular inhibition, noted here, may be another line of defense. We have proposed that the inhibition may be the result of competition between HIV-1 and HIV-2 for cellular factors, possibly involving the long terminal repeats (LTRs). For safety reasons, it may be advantageous to use subunits of HIV-2 for vaccines and gene therapy. HIV-2, specifically noncytopathic HIV-2, could be viewed as an attenuated HIV-1 vaccination model. HIV-2-derived gene transfer vectors may not only be inhibitory themselves but also allow for the insertion of additional protective genes to aim at multiple targets in the HIV-1 life cycle, thus curtailing the evolution of escape mutants.

Antibiosis↗
PubMed2001

Eosinophils, eosinophil ribonucleases, and their role in host defense against respiratory virus pathogens.

Eosinophils remain among the most enigmatic of cells, as our appreciation of their detrimental activities--e.g., asthma and allergic disease--far outweighs our understanding of their beneficial effects. Among the major secretory effector proteins of eosinophils are the ribonucleases eosinophil-derived neurotoxin (EDN) and eosinophil cationic protein (ECP) in primates and their orthologs, the eosinophil-associated ribonucleases (EARs) in rodents. The rapid diversification observed among these ribonucleases suggested that the ultimate target(s) might be similarly efficient at generating sequence diversity while maintaining an unalterable susceptibility to ribonucleolytic cleavage. This has prompted us to consider a role for these proteins and by extension, for eosinophils, in host defense against single-stranded RNA virus pathogens. We detail our studies of the antiviral activity of eosinophils and eosinophil ribonucleases against respiratory syncytial virus (RSV) in vitro and the related, natural rodent pathogen, pneumonia virus of mice (PVM), in vivo, and consider the possibility that antiviral host defense and the dysregulated responses leading to asthma represent opposing sides of an eosinophil-mediated double-edged sword.

Animals↗
PubMed2005

Occurrence of a DNA sequence of a non-retro RNA virus in a host plant genome and its expression: evidence for recombination between viral and host RNAs.

This study demonstrates that sequences homologous to those of the non-retro RNA virus (Potato virus Y; PVY) are integrated into the genome of several grapevine varieties. The integrated PVY-coat-protein-like cistron is expressed in the grapevine as indicated by Southern and Western blot analyses as well as by RNase protection assay. In addition, genome-walking studies showed that one PVY-like sequence is flanked by 41-bp direct repeats and is embedded in authentic grapevine sequences, flanked by inverted repeats. Rearranged PVY-like sequences were also found in tobacco. It is suggested that nonhomologous recombination of a potyviral RNA with RNA of a retrotransposable element took place at some point in evolution. The initial integration locus was probably within a grapevine gene homologous to a pentatricopeptide repeat-carrying protein, and was later transposed to other locations. The current location is reminiscent of a MITE-type retroelement, indicating transposition history. Because grapevine cultivars are propagated asexually, without going through a meiotic phase, the chance for DNA recombination is minimal and the foreign integrated sequence may be better conserved, enabling it to be expressed correctly in the recipient genome.

Amino Acid Sequence↗
PubMed1997

Sequence and phylogenetic analysis of the cytoplasmic inclusion protein gene of zucchini yellow mosaic potyvirus: its role in classification of the Potyviridae.

The cytoplasmic inclusion (CI) gene of a Singapore isolate of zucchini yellow mosaic virus (ZYMV-S) was sequenced and compared with CI of 14 other potyviruses. In addition to the consensus sequence GAVGSGKST of nucleotide binding motif (NTBM) which is implicated as a membrane-binding component of the RNA helicase complex, five other conserved motifs were found. Phylogenetic trees were constructed from sequence data for the CI and the coat protein. Similar branching patterns obtained from both CI and coat protein analyses suggests that phylogenetic relationship among potyviruses can be determined using the CI. We propose that phylogenetic analysis of CI gene may be used as an alternative approach for the study of evolution within the family Potyviridae.

Amino Acid Sequence↗
PubMed2007

Patterns of recombination in turnip mosaic virus genomic sequences indicate hotspots of recombination.

Potyviruses have variable single-stranded RNA genomes and many show clear evidence of recombination. This report studied the distribution of recombination sites in the genomes of 92 isolates of the potyvirus Turnip mosaic virus (TuMV); 42 came from the international gene sequence databases and an additional 50 complete genomic sequences were generated from field samples collected in Europe and Asia. The sequences were examined for evidence of recombination using seven different sequence comparison methods and the exact position of each site was confirmed by sequence composition analysis. Recombination sites were found throughout the genomes, except in the small 6K1 protein gene, and only 24 of the genomes (26%) showed no evidence of recombination. Statistically significant clusters of recombination sites were found in the P1 gene and in the CI/6K2/VPg gene region. Most recombination sites were bordered by an upstream (5') region of GC-rich and downstream (3') region of AU-rich sequence of a similar length. Correlations between the presence and type of recombination site and provenance, host type and phylogenetic relationships are discussed, as is the role of recombination in TuMV evolution.

Genome, Viral↗
PubMed1994

Nucleotide sequence comparison of the membrane protein genes of three enterotropic strains of mouse hepatitis virus.

The nucleotide sequences of the membrane (M) protein genes and their deduced amino acid sequences of three enterotropic strains of the coronavirus mouse hepatitis virus (MHV) -Y, -RI and -DVIM were determined and compared with the previously reported sequences of two respiratory MHV strains -A59 and -JHM. The five MHV strains shared extensive nucleotide (95.2-99.0%) as well as amino acid homology (95.6-98.7%). A variable region, including a 15 nucleotide deletion unique to MHV-RI, could be identified at the 5'-terminus of the gene. This region of the M protein may be immunogenic and may contribute to the antigenic diversity of the MHV strains. Sequence relationships between the strains showed no correspondence with the primary cell tropism. This may suggest that evolution of enterotropism was not a single occurrence among different MHV strains. No sequence unique to either tropism group could be identified, indicating that the M protein of MHV probably has no part in the determination of MHV tissue tropism.

Amino Acid Sequence↗
PubMed2005

A genotypic assay for the amplification and sequencing of gag and protease from diverse human immunodeficiency virus type 1 group M subtypes.

In human immunodeficiency virus type 1 (HIV-1), an interaction exists between the in vivo evolution of Gag protein and protease to escape from antiretroviral drug selective pressure. Therefore, it was decided to develop a genotypic assay for the amplification and sequencing of HIV-1 gag and protease. As the HIV-1 pandemic is characterised by a large genetic diversity, the assay developed was evaluated on a panel of 28 genetically divergent samples belonging to the following subtypes A1, B, C, D, F1, F2, G, H, J, CRF01-AE, CRF02-AG and CRF13-cpx. The assay displayed a detection limit ranging between 500 RNA copies/ml and 5000 RNA copies/ml plasma. Full-length sequences could be obtained for 25 samples. The population sequences of the three other samples lacked a part of the sequence because of heterogeneous signal, probably due to the presence of quasi-species with insertions/deletions of a different length.

DNA Primers↗
PubMed2004

Orthoreovirus and Aquareovirus core proteins: conserved enzymatic surfaces, but not protein-protein interfaces.

Orthoreoviruses and Aquareoviruses constitute two respective genera in the family Reoviridae of double-stranded RNA viruses. Orthoreoviruses infect mammals, birds, and reptiles and have a genome comprising 10 RNA segments. Aquareoviruses infect fish and have a genome comprising 11 RNA segments. Despite these differences, recent structural and nucleotide sequence evidence indicate that the proteins of Orthoreoviruses and Aquareoviruses share many similarities. The focus of this review is on the structure and function of the Orthoreovirus core proteins lambda1, lambda2, lambda3, and sigma2, for which X-ray crystal structures have been recently reported. The homologous core proteins in Aquareoviruses are VP3, VP1, VP2, and VP6, respectively. By mapping the locations of conserved residues onto the Orthoreovirus crystal structures, we have found that enzymatic surfaces involved in mRNA synthesis are well conserved between these two groups of viruses, whereas several surfaces involved in protein-protein interactions are not well conserved. Other evidence indicates that the Orthoreovirus mu2 and Aquareovirus VP5 proteins are homologous, suggesting that VP5 is a core protein as mu2 is known to be. These findings provide further evidence that Orthoreoviruses and Aquareoviruses have diverged from a common ancestor and contribute to a growing understanding of the functions of the core proteins in viral mRNA synthesis.

Amino Acid Sequence↗
PubMed2004

Evolution of genotypic and phenotypic resistance to Enfuvirtide in HIV-infected patients experiencing prolonged virologic failure.

Four heavily antiretroviral-experienced HIV-infected patients had significant plasma HIV-RNA reductions (>1 log) after beginning an Enfuvirtide (ENF)-based rescue regimen. However, all had viral rebound shortly thereafter, sustaining high levels of plasma viremia over 80 weeks. These patients developed rapidly genotypic and phenotypic resistance to ENF. Mutations within the HR1 env region were selected (N43D in three and G36V/D in one), resulting in high-level phenotypic resistance to ENF. Interestingly, two patients had a sustained CD4+ T-cell increase and two maintained stable CD4+ T-cell counts despite virologic failure under ENF. The possible mechanisms involved in this response were examined. Changes in virus tropism from R5 to R5/X4 were observed in two patients, in parallel with increases in ENF phenotypic resistance. Low levels of T-cell activation, T-cell turnover, and cytotoxic T lymphocyte (CTL) activity were found in all four patients. An overall increase in the proportion of viruses released from cells of the macrophage lineage was observed. In summary, single mutations at the HR1 env region result in significant loss of susceptibility to ENF. Despite virologic failure, these patients may maintain elevated CD4+ counts through a reduction in their overall immune activation.

Amino Acid Sequence↗
PubMed2002

Phylogeny of New World arenaviruses based on the complete coding sequences of the small genomic segment identified an evolutionary lineage produced by intrasegmental recombination.

Previous studies suggested that the small genomic segments (S-RNA) of the South American arenaviruses (SA-AVs) represent three phylogenetic lineages (designated A, B, and C) and indicated that the S-RNA of Whitewater Arroyo virus (WWAV) (a North American arenavirus [NA-AV]) is a product of genetic recombination between a lineage A and lineage B virus. The purpose of this study was to extend our knowledge on the phylogenetic relationships between WWAV, the two other NA-AVs (Tamiami and bear canyon), and the 15 SA-AVs. Therefore, we determined the complete sequence of the S-RNA of nine arenaviruses previously uncharacterized or sequenced only partially. Phylogenetic analyses of the two complete coding regions indicated that the S-RNA of the three NA-AVs have descended from a single ancestral virus, which was the product of recombination between a lineage A and lineage B arenavirus. No such evidence for genetic recombination was found in cupixi virus (a novel arenavirus isolated from a wild rodent captured in Northeastern Brazil) or the 14 other SA-AVs. The recombinant nature of the S-RNA of NA-AVs distinguishes them from the SA-AVs, and thus, indicates that the NA-AVs represent a fourth phylogenetic lineage in the Tacaribe serocomplex.

Amino Acid Sequence↗
PubMed1987

The four classes of endogenous murine leukemia virus: structural relationships and potential for recombination.

The process by which leukemogenic viruses are generated during the lifetime of certain strains of mice is poorly understood. We have therefore set out to define all the murine leukemia virus-related endogenous proviruses of HRS/J mice. We have cloned 34 different proviral fragments and their flanking cellular sequences. These have been characterized by restriction enzyme analysis, by fingerprinting in vitro-synthesized RNA, and by DNA sequencing. We conclude that all the proviruses can be assigned into one of four different classes: the previously characterized ecotropic, xenotropic, and polytropic viruses, as well as a new class we have termed modified polytropic viruses. The xenotropic, polytropic, and modified polytropic classes are closely related to one another, but as a group they differ considerably from the ecotropic class. Sequence analyses show that both polytropic and modified polytropic sequences can contribute env sequences to recombinant viruses.

Animals↗
PubMedDate not supplied

[The importance of the Epstein-Barr virus and other viruses in the evolution of human host homeostatic systems].

There is a great number (150) DNA sequence homology with genes and mRNA of man. They are involved in expression of biological active matters, which are participate in homeostasis of host. This is an evidence of a long-time co-evolution EBV and host-man populations. It play a great role in a vertical and horizontal dissemination some important for homeostasis genes of man.

Biological Evolution↗
PubMed2004

Adaptation to the deleterious effects of antimicrobial drug resistance mutations by compensatory evolution.

Compensatory mutations, due to their ability to mask the deleterious effects of another mutation, are important for the adaptation and evolution of most organisms. Resistance to antibiotics, antivirals, antifungals, herbicides and insecticides is usually associated with a fitness cost. As a result of compensatory evolution, the initial fitness costs conferred by resistance mutations (or other deleterious mutations) can often be rapidly and efficiently reduced. Such compensatory evolution is potentially of importance for (i) the long-term persistence of drug resistance, (ii) reducing the rate of fitness loss associated with the accumulation of deleterious mutations in small asexual populations, and (iii) the evolution of complexity of cellular processes.

Amino Acid Sequence↗