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PubMed1982

Transforming gene of a human leukaemia cell is unrelated to the expressed tumour virus related gene of the cell.

The virally encoded oncogenes (v-onc) of avian and mammalian retroviruses are the recombinant products of normal cellular genes (c-onc) and a retroviral genome. These cellular homologues have been highly conserved during evolution and are found in human DNA. The expression of at least one c-onc under the control of a viral promoter results in transformation of cells in a manner resembling that displayed by the v-onc counterpart; the inappropriate expression of c-onc in the absence of viral influences could likewise result in the malignant state. This proposal would be strongly supported by the presence of c-onc RNAs in a variety of human tumours were they not also demonstrable in normal tissues. The role of these RNAs in the oncogenic process remains unclear. Here we report that RNA homologous to the oncogene (v-abl) of Abelson murine leukaemia virus (A-MLV) is expressed in a unique human leukaemia in a fashion different from that of other human tissues and tumours. In addition, DNA from this tumour transforms NIH-3T3 cells at a high efficiency in a transfection assay. The transfected sequences are not related to the v-abl gene, but the NIH-3T3 transformants manufacture a transforming growth factor which behaves similarly to factors produced by A-MLV-transformed NIH-3T3 fibroblasts.

Abelson murine leukemia virus↗
PubMed2000

Evolution of human and non-human primate CC chemokine receptor 5 gene and mRNA. Potential roles for haplotype and mRNA diversity, differential haplotype-specific transcriptional activity, and altered transcription factor binding to polymorphic nucleotides in the pathogenesis of HIV-1 and simian immunodeficiency virus.

Polymorphisms in CC chemokine receptor 5 (CCR5), the major coreceptor of human immunodeficiency virus 1 (HIV-1) and simian immunodeficiency virus (SIV), have a major influence on HIV-1 transmission and disease progression. The effects of these polymorphisms may, in part, account for the differential pathogenesis of HIV-1 (immunosuppression) and SIV (natural resistance) in humans and non-human primates, respectively. Thus, understanding the genetic basis underlying species-specific responses to HIV-1 and SIV could reveal new anti-HIV-1 therapeutic strategies for humans. To this end, we compared CCR5 structure/evolution and regulation among humans, apes, Old World Monkeys, and New World Monkeys. The evolution of the CCR5 cis-regulatory region versus the open reading frame as well as among different domains of the open reading frame differed from one another. CCR5 cis-regulatory region sequence variation in humans was substantially higher than anticipated. Based on this variation, CCR5 haplotypes could be organized into seven evolutionarily distinct human haplogroups (HH) that we designated HHA, -B, -C, -D, -E, -F, and -G. HHA haplotypes were defined as ancestral to all other haplotypes by comparison to the CCR5 haplotypes of non-human primates. Different human and non-human primate CCR5 haplotypes were associated with differential transcriptional regulation, and various polymorphisms resulted in modified DNA-nuclear protein interactions, including altered binding of members of the NF-kappaB family of transcription factors. We identified novel CCR5 untranslated mRNA sequences that were conserved in human and non-human primates. In some primates, mutations at exon-intron boundaries caused loss of expression of selected CCR5 mRNA isoforms or production of novel mRNA isoforms. Collectively, these findings suggest that the response to HIV-1 and SIV infection in primates may have been driven, in part, by evolution of the elements controlling CCR5 transcription and translation.

Animals↗
PubMed2006

Molecular evidence of HTLV-II subtype B among an urban population living in South Brazil.

Human T cell lymphotropic virus type II (HTLV-II) is a deltaretrovirus endemic in Indian populations living in Central and South America, among Pygmies tribes from Central Africa, and epidemic among injecting drug users (IDUs) in the United States, Europe, Southeast Asia, and South America. To date only the HTLV-IIa subtype has been demonstrated among Brazilians (Amazon basin Indians, blood donors, and IDUs). We analyzed HTLV-II isolates from 12 individuals living in the urban area of Porto Alegre, Southern Brazil, identified as seropositive for HTLVI/II in a blood donation. The HTLV-II long terminal repeat (LTR) region was sequenced and compared with nucleotide sequences of isolates HTLV-IIa (Mo), HTLV-IIb (NRA) prototypes. Phylogenetic analysis of the LTR region demonstrated that seven new isolates clustered together with American Indians HTLV-IIb isolates, and five new HTLV-IIa isolates clustered within the HTLV-IIa Brazilian subgroup, named the HTLV-IIc subtype. Both HTLV-IIa and IIb seem to be endemic in the urban area of Porto Alegre, South of Brazil, and could have reached this region via the Amazon basin and the Pacific Coast ancient human migratory pathways. To our knowledge this is the first study demonstrating the presence of HTLV-IIb among the urban population in Brazil.

Base Sequence↗
PubMed1982

The biology and chemistry of Epstein-Barr virus.

Epstein-Barr virus (EBV) is the human prototype of a family of closely related herpesviruses of Old World primates. These agents probably evolved and spread among the Old World primates since the divergence of apes from monkeys about 30 million years ago. Although the DNAs of the EBV family have no sequence homology to other herpesviruses, there are some features in common with other herpesviral genomes. EBV DNA is unusual in having five tandem direct repeat elements which divide the genome into five unique sequence domains. The tandem direct repeats at the ends of the linear virion DNA probably mediate circularization of the viral DNA to form the circular episomal viral DNA which is characteristic of EBV-infected cells. In latent transforming infection, messenger RNAs are encoded by three widely separate regions of the EBV genome. The remainder of the viral genome encodes many RNAs and proteins which are expressed in productive infection. Early and late viral genes are intermixed along the full length of EBV DNA.

Animals↗
PubMed1994

The polymerase chain reaction and hepatitis C virus diagnosis.

In the absence of tissue culture, electron microscopy or assays for viral antigen, the direct detection of hepatitis C virus (HCV) is by necessity dependent upon nucleic acid hybridisation methods. Of the available methods, amplification of HCV cDNA by polymerase chain reaction (PCR) commends itself by virtue of its extreme sensitivity and its consequent ability to detect the very low levels of HCV-RNA that are present in many clinical samples. In this review the development and evolution of PCR techniques for HCV detection are described and a number of clinical applications are considered in detail. The applications include diagnosis of acute infection during the seronegative window period prior to the appearance of HCV antibodies, and diagnosis of HCV infection in the immunosuppressed. PCR also enables identification of the chronic viraemic carrier state and it permits accurate monitoring of the antiviral effects of drugs such as interferon. Confirmation of the specificity of HCV antibody assays and detection of HCV contamination of blood donations and blood products are other important areas in which PCR techniques have proved invaluable. In addition, PCR-based techniques underlie an increasing number of molecular epidemiological and genotyping studies and they are providing insights into the details of HCV cellular tropism and replication. A number of logistic problems and operational difficulties are also discussed. Despite these limitations it is concluded that PCR will continue to make significant contributions to both clinical practice and to our understanding of the basic biology of HCV infection.

Blood Donors↗
PubMed1988

Nucleotide sequence and expression of rabbit globin genes zeta 1, zeta 2, and zeta 3. Pseudogenes generated by block duplications are transcriptionally competent.

The addition of two embryonic globin genes, zeta 0 and zeta 4, to the rabbit alpha-like globin gene cluster expands it to include eight genes arranged 5'-zeta 0-zeta 1-alpha 1-theta 1-zeta 2-zeta 3-theta 2-zeta 4-3'. The identification of these new genes supports the model that this gene cluster evolved by a series of block duplications of gene sets. The nucleotide sequence of three embryonic zeta-globin genes, zeta 1, zeta 2, and zeta 3, shows that all three are pseudogenes. Gene zeta 1 contains two frame-shift deletions, gene zeta 2 has lost exon 1 as well as the 5' promoter sequences, and gene zeta 3 has lost and replaced codons for amino acids that are critical for the function of alpha- and zeta-globin polypeptides. However, genes zeta 1 and zeta 3 are still transcriptionally competent, as shown by the accurate initiation and processing of transcripts from cloned genes introduced into HeLa cells. A quantitative comparison of the zeta-globin gene sequences indicates that the ancestor to the rabbit zeta 1 and zeta 3 genes was inactivated about 44 million years ago, and the block duplication that formed the two genes occurred about 28 million years ago. About 600 base pairs of the 5'-flanking sequence of the rabbit zeta 3-globin gene is very similar to the 5' flanks of three other mammalian zeta-globin genes.

Animals↗
PubMed1995

Primary structure and sequence analysis of RNA2 of a mechanically transmitted barley mild mosaic virus isolate: an evolutionary relationship between bymo- and furoviruses.

The RNA2 nucleotide sequence of a mechanically transmitted isolate of barley mild mosaic virus (BaMMV) has been determined. A combination of Northern blot and sequence analysis indicates that this RNA2 lacks approximately 1000 nucleotides of its C-terminal protein (P2) gene, with respect to Polymyxa graminis transmitted BaMMV. This is confirmed by sequence comparison with RNA2 of a fungus transmitted BaMMV isolate, which reveals the presence of a single deletion located in the 3'-terminal part of the P2 gene. As a consequence, this RNA2 codes for a P2 protein of only 34 K. Sequence homology between the bymovirus P2 protein and the capsid readthrough protein of beet necrotic yellow vein virus and soil-borne wheat mosaic virus suggests an evolutionary relationship between bymo- and furoviruses.

Amino Acid Sequence↗
PubMed1995

Stability of replicative form and fitness among RNA variants transcribed by Qbeta replicase.

Stability in the replicative form of RNA molecules transcribed by Qbeta replicase was demonstrated to provide a sequence-dependent indicator of their fitness. This follows from the finding that replication rates reported for 17 RNA species (genome length, 77-370 nucleotides) correlate with the self-interaction free energy of these self-annealed strands. Formation of double-stranded molecules during replication conversely decreased with self-interaction free energy. H-bond formation between self-complementary segments of folded RNA molecules plainly produces a potential energy barrier opposing the transition to a double-stranded, non-replicating form. Melting point temperature and resistance of RNA synthesis to elevated salt levels among three variants also increased with strand configuration free energy. Genome-based estimates of fitness in other self-replicating RNA species were therefore possible. Once a link between the kinetic parameters of replication and base sequence of these RNA species is adequately established, estimates of fitness can be dissociated from survival states following evolution, and Darwin's fundamental precept, 'survival of the fittest,' could be appraised as an experimentally testable hypothesis.

Allolevivirus↗
PubMed2006

Comparison of 3'-end encoding regions of turkey coronavirus isolates from Indiana, North Carolina, and Minnesota with chicken infectious bronchitis coronavirus strains.

OBJECTIVE: To analyze the 3'-end structural protein-encoding region of turkey coronavirus (TCoV) isolates associated with outbreaks of acute enteritis in Indiana, North Carolina, or Minnesota. METHODS: Four isolates of TCoV were sequenced over the entire 3'-end structural protein-encoding region and compared phylogenetically along with the corresponding sequences of infectious bronchitis virus (IBV) strains. RESULTS: The sequence similarity between TCoV and IBV was lower than that among TCoV isolates or that among IBV strains. The variation of sequences between TCoV and IBV was mainly contributed by the S protein gene. The sequence similarity of S gene between TCoV and IBV was lower than that among TCoV isolates or that among IBV strains. The phylogenetic tree based on the S protein region was similar to that based on the entire 3'-end structural protein-encoding region with TCoV isolates and IBV strains grouped in two separate clusters. The phylogenetic tree based on other genes had a very different topology with TCoV isolates randomly forming groups with different IBV strains. CONCLUSIONS: These results suggested that TCoV probably shared the same origin with that of IBV and acquired sequences of S gene for turkey intestine tropism during the process of evolution in a separate environment.

Animals↗
PubMed2005

Viruses - seeking and destroying the tumor program.

DNA viruses have enormous utility in cancer research, both as tools for tumor target discovery as well as agents for lytic cancer therapies. This is because there is a profound functional overlap between the DNA viral and tumor cell programs. DNA viruses encode proteins that elicit growth deregulation in infected cells similar to that engendered by mutations in tumor cells. Evolution has refined viral proteins to target the critical cellular hubs that regulate growth. Thus, viral proteins are discriminating biochemical probes that can be used to identify and characterize novel tumor targets. Moreover, the overlap between the DNA viral and tumor programs can also be exploited for the development of lytic cancer therapies. Discovering whether tumor cells selectively complement the replication of viral mutants can reveal novel oncolytic viral therapies, as well as unexpected tumor properties. For example, altered RNA export was recently uncovered as a novel tumor cell property that underlies ONYX-015 replication, a promising oncolytic adenoviral therapy. A perspective is provided on how adenovirus could be systematically exploited to map the requisite role, or indeed the redundancy, of cellular pathways that act in an integrated program to elicit pathological replication. This knowledge has important applications for the rational design of the next generation of oncolytic viruses, as well as the discovery of efficacious combination cancer therapies.

Adenoviridae↗
PubMed2001

Systemic spread of an RNA insect virus in plants expressing plant viral movement protein genes.

Flock house virus (FHV), a single-stranded RNA insect virus, has previously been reported to cross the kingdom barrier and replicate in barley protoplasts and in inoculated leaves of several plant species [Selling, B. H., Allison, R. F. & Kaesberg, P. (1990) Proc. Natl. Acad. Sci. USA 87, 434-438]. There was no systemic movement of FHV in plants. We tested the ability of movement proteins (MPs) of plant viruses to provide movement functions and cause systemic spread of FHV in plants. We compared the growth of FHV in leaves of nontransgenic and transgenic plants expressing the MP of tobacco mosaic virus or red clover necrotic mosaic virus (RCNMV). Both MPs mobilized cell-to-cell and systemic movement of FHV in Nicotiana benthamiana plants. The yield of FHV was more than 100-fold higher in the inoculated leaves of transgenic plants than in the inoculated leaves of nontransgenic plants. In addition, FHV accumulated in the noninoculated upper leaves of both MP-transgenic plants. RCNMV MP was more efficient in mobilizing FHV to noninoculated upper leaves. We also report here that FHV replicates in inoculated leaves of six additional plant species: alfalfa, Arabidopsis, Brassica, cucumber, maize, and rice. Our results demonstrate that plant viral MPs cause cell-to-cell and long-distance movement of an animal virus in plants and offer approaches to the study of the evolution of viruses and mechanisms governing mRNA trafficking in plants as well as to the development of promising vectors for transient expression of foreign genes in plants.

Biological Transport↗
PubMed2006

An intron with a constitutive transport element is retained in a Tap messenger RNA.

Alternative splicing is a key factor contributing to genetic diversity and evolution. Intron retention, one form of alternative splicing, is common in plants but rare in higher eukaryotes, because messenger RNAs with retained introns are subject to cellular restriction at the level of cytoplasmic export and expression. Often, retention of internal introns restricts the export of these mRNAs and makes them the targets for degradation by the cellular nonsense-mediated decay machinery if they contain premature stop codons. In fact, many of the database entries for complementary DNAs with retained introns represent them as artefacts that would not affect the proteome. Retroviruses are important model systems in studies of regulation of RNAs with retained introns, because their genomic and mRNAs contain one or more unspliced introns. For example, Mason-Pfizer monkey virus overcomes cellular restrictions by using a cis-acting RNA element known as the constitutive transport element (CTE). The CTE interacts directly with the Tap protein (also known as nuclear RNA export factor 1, encoded by NXF1), which is thought to be a principal export receptor for cellular mRNA, leading to the hypothesis that cellular mRNAs with retained introns use cellular CTE equivalents to overcome restrictions to their expression. Here we show that the Tap gene contains a functional CTE in its alternatively spliced intron 10. Tap mRNA containing this intron is exported to the cytoplasm and is present in polyribosomes. A small Tap protein is encoded by this mRNA and can be detected in human and monkey cells. Our results indicate that Tap regulates expression of its own intron-containing RNA through a CTE-mediated mechanism. Thus, CTEs are likely to be important elements that facilitate efficient expression of mammalian mRNAs with retained introns.

Alternative Splicing↗
PubMed2002

Factors related to the chronicity and evolution of hepatitis C infection in patients co-infected by the human immunodeficiency virus.

OBJECTIVES: This work analyses the influence of immune status, serum human immunodeficiency virus (HIV) load and hepatitis C virus (HCV) genotypes on the probability of resolution of HCV infection in HIV-co-infected patients, as well as the evolution of HCV viremia after antiretroviral therapy. PATIENTS AND METHODS: Forty-five patients with anti-HIV and anti-HCV antibodies were classified into two groups as a function of the positivity or persistent negativity of HCV RNA detection (active or recovered HCV infection, respectively). They were treated with highly active antiretroviral therapy (HAART). Serum HCV RNA was quantified by the reverse transcription-polymerase chain reaction. HCV genotypes were detected by line probe assay or by detection of type-specific antibodies. RESULTS: HCV RNA was detectable in 30 (66.6%) out of 45 HIV-infected patients. CD4+ T-cell counts, HIV viremia, or HCV genotypes were similar in patients with active or recovered HCV infection. Patients with active HCV infection had a non-significant decrease of HCV viremia during a follow-up of 12 months (from 6.15 +/- 6.32 to 5.96 +/- 6.05 log copies/mL). This was not influenced by baseline HCV or HIV viral load, HCV genotype, or CD4+ T-cell count. The non-significant decrease was present in patients with or without an immunological response to HAART. CONCLUSION: HCV genotypes, immune status, or serum HIV load did not influence the resolution or chronicity of HCV infection in HIV-co-infected individuals. A non-significant decrease of HCV viremia in these patients treated with combinations including antiproteases could be expected.

Adult↗
PubMedDate not supplied

[Chronic viral hepatitis C. Part 1. General considerations].

Hepatitis C virus was identified in 1989 as the main causative agent of non-A, non-B and was followed by the recognition of a high prevalence of hepatitis C virus infection after transfusion of infected blood or blood products and in association with intravenous drug abuse. The availability of sensitive and reliable techniques to screen blood for hepatitis C virus has reduced the incidence of post-transfusion hepatitis. True healthy carriers of hepatitis C virus did not exist. Approximately 95% of hepatitis C virus infected individuals can be identified by third generation anti-hepatitis C virus testing. Retrospective studies of iatrogenic hepatitis C virus infection are the main source of the natural history of the disease. The distribution of different hepatitis C virus genotypes varies according to the geographic region. In South America, Europe, The United States and Japan hepatitis C virus genotypes 1, 2 and 3 account for the majority of the infections, being (sub)type 1b the most prevalent. Epidemiological parameters (age, risk factors and duration of infection) may be associated with hepatitis C virus genotypes (intravenous drug abuse with types 1-a and 3-a and 1-b with post-transfusion hepatitic C). Subtype 1-b, lead to a more severe course of viral infection, with ultrastructural alterations of the mitochondria, and greater impairment of the process of oxidative phosphorylation. No increased production of free radicals may influence the evolution of the liver disease by an enhancement of the cytopathic effect of hepatitis C virus. The clinical significance of intrahepatic hepatitis C virus level in patients with chronic hepatitis C virus infection is not determined by host factors (age of patient, mode or duration of infection) or by virus factors (hepatitis C virus genotypes) and, repeatedly negative RT-PCR for hepatitis C virus RNA in serum does not indicate absence of hepatitis C virus from the liver. The association between autoimmunity and hepatitis C virus is questioned. Markers of its does occur with high frequency in these patients. Modulation of immune responses to hepatitis C virus envelope E2 protein following injection of plasmid DNA, has been used for induction of specific response to hepatitis C virus. The spectrum of such responses could likely be broadened by combining plasmids, delivery routes, and other forms of encoded immunogens (peptide vaccines). These may be important to the development of a vaccine against the high mutable hepatitis C virus. The pathogenic role of novel DNA virus (TTV) is under spotlight. As with hepatitis G, however, the association of TTV with disease is far from clear.

Hepacivirus↗
PubMed1996

[Molecular biology of enteroviruses].

Molecular biological methods offer new approaches to the study of RNA viruses. On the example of enteroviruses we tried to give an account, of recent progress in the knowledge and understanding of these important human pathogens. Firstly concerning their structural and genomic organisation; secondly as regards understanding of their pathology and pathogenicity; thirdly the impact of such methods on rapid, sensitive and specific diagnosis, treatment, on epidemiology and finally on evolution and classification of the large picornavirus family where the enterovirus genus belongs. We believe that molecular biology will elucidate still unknown features of enteroviruses, which are not yet correctly evaluated human pathogens.

Enterovirus↗
PubMed2000

Cross-genotypic interaction between hepatitis C virus NS3 protease domains and NS4A cofactors.

BACKGROUND/AIMS: Hepatitis C virus (HCV) nonstructural protein 3 (NS3) protease requires NS4A as a cofactor. This cofactor activity has been mapped to the central region of NS4A which interacts with the N-terminus of NS3 protease. To investigate whether this interaction is conserved among different genotypes of HCV cross-genotypic characterization were performed to delineate the importance of NS4A cofactor function in relation to the molecular evolution of HCV METHODS: Active NS3 protease domains of genotype 1-3 (representing five subtypes: la, 1b, 2a, 2b and 3a) were produced and purified from bacterial cells. NS4A cofactor-dependent in vitro trans cleavage assays were established using the in vitro translated recombinant protein substrates. These substrates contained the junction site of NS4A/NS4B, NS4B/NS5A or NS5A/NS5B. RESULTS: Our data revealed that NS3 proteases cross-interacted with NS4A cofactors derived from different genotypes, although the genotype 2 cofactor was less efficient, which could be due to greater genetic variations in this region. Furthermore, the corresponding region in hepatitis G virus (HGV) NS4A was found to provide weak cofactor activity for HCV NS3 protease. Surprisingly, a synthetic substrate peptide from the NS4B/NS5A junction was also found to enhance HCV NS3 protease activity in a dose-dependent manner. CONCLUSION: Our study suggests that the NS4A cofactor function is well conserved among HCV It is likely that other HCV-related viruses may have developed similar strategies to regulate their protease activity.

Evolution, Molecular↗
PubMed1986

Antigenic and molecular evolution of the vaccine strain of type 3 poliovirus during the period of excretion by a primary vaccinee.

A 4 month old child was immunized with a vaccine containing the Sabin live attenuated vaccine strains of all three serotypes of poliovirus. The antigenic and molecular evolution of the Sabin strain of poliovirus type 3 was then followed throughout the entire period of virus excretion. Novel strains appeared at 8, 42 and 52 days post-vaccination and were the products of both intertypic recombination between type 2 and type 3 poliovirus in regions of the genome coding for non-structural proteins and of point mutations in the region coding for the structural proteins. Excretion of virus continued for 73 days. All strains examined reacted with all monoclonal antibodies specific for the main immunodominant antigenic site of type 3 poliovirus, but variation was observed at other, immunorecessive sites. These findings have possible implications for the evolution of the virus in vaccinees or in epidemics and are consistent with the known antigenic stability of the virus.

Antibodies, Monoclonal↗