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C Vink

Publications and source records attributed to C Vink.

At least 37 records · Page 2Linked to original sources
PubMed1997

Cloning and functional characterization of the origin of lytic-phase DNA replication of rat cytomegalovirus.

A cis-acting sequence within the rat cytomegalovirus (RCMV) genome (oriLyt) that directs initiation of lytic-phase DNA replication is identified in this report. RCMV oriLyt was localized within a 4.3 kb NcoI fragment that is situated immediately upstream of the gene encoding the major DNA-binding protein. The activity of oriLyt was investigated in a transient replication assay, in which the ability of plasmid constructs to promote DNA replication was tested. Replication of oriLyt-containing plasmids was autonomous and resulted in the generation of high-molecular-mass concatemers of head-to-tail-linked plasmid oligomers. oriLyt-mediated replication was found to depend on viral DNA polymerase activity supplied by RCMV infection. The sequence required for oriLyt function was found to reside within a 3.3 kb HincII-NcoI fragment. The RCMV oriLyt sequence is highly complex, containing 23 direct repeats (DRs) and 16 inverted repeats (IRs) of lengths greater than 10 bp. Two of the DRs (DR21 and DR22) are exceptionally large, being 80 and 88 bp in length, respectively. In addition, two sequence elements (of 127 and 120 bp) with dyad symmetry were identified within oriLyt. Although the sequence similarity of RCMV oriLyt with its human cytomegalovirus counterpart is limited, there is a striking resemblance in the overall organization of several IRs and DRs within both sequences.

Animals↗
PubMed1997

Patients' perceptions of outcomes of a Canadian hospitalization.

Notes that with health care reform moving at tremendous speed throughout Canada, a great deal of interest in outcomes research has been generated. States that the research team consisted of 17 professional practice leaders from eight disciplines. Proposes, through the research, to identify from the perspective of former patients what results they hoped to achieve prior to discharge from hospital and what facilitated and hindered them in achieving these results. Reports that a representative sample was selected for the study. Forty-one former patients each participated in up to two focus groups, with a total of 16 focus groups conducted. Hierarchical analysis revealed themes that fell within the framework of structure, process and outcomes. The findings will assist in ensuring that more appropriate and effective care is offered to patients by a variety of disciplines.

Adult↗
PubMed1996

Cloning and sequence analysis of the genes encoding DNA polymerase, glycoprotein B, ICP18.5 and major DNA-binding protein of rat cytomegalovirus.

In all herpesviruses a block of genes is present which is composed of the genes encoding DNA polymerase, glycoprotein B (gB), ICP18.5 and major DNA-binding protein (MDBP). Here we report the cloning and sequencing of this gene block from rat cytomegalovirus (RCMV). The gene block spans 13.3 kbp and contains the four genes in the order pol, gB, ICP18.5 and MDBP. A similar order of genes has previously been reported for human and murine cytomegaloviruses. The pol, gB, ICP18.5 and MDBP genes contain open reading frames which have the capacity to encode proteins of 1120, 914, 893 and 1281 amino acids, respectively. Comparison of the predicted amino acid sequences of the four RCMV proteins with the corresponding proteins of other herpesviruses revealed a close relationship between RCMV and other cytomegaloviruses, which corroborates the usefulness of the RCMV-rat model for studying cytomegalovirus biology.

Amino Acid Sequence↗
PubMed1996

Structure of the rat cytomegalovirus genome termini.

The lytic replication cycle of herpesviruses can be divided into the following three steps: (i) circularization, in which, after infection, the termini of the linear double-stranded viral genome are fused; (ii) replication, in which the circular DNA serves as template for DNA replication, which generates large DNA concatemers; and (iii) maturation, in which the concatemeric viral DNA is processed into unit-length genomes, which are packaged into capsids. Sequences at the termini of the linear virion DNA are thought to play a key role in both genome circularization and maturation. To investigate the mechanism of these processes in the replication of rat cytomegalovirus (RCMV), we cloned, sequenced, and characterized the genomic termini of this betaherpesvirus. Both RCMV genomic termini were found to contain a single copy of a direct terminal repeat (TR). The TR sequence is 504 bp in length, has a high GC content (76%), and is not repeated at internal sites within the RCMV genome. The TR comprises several small internal direct repeats as well as two sequences which are homologous to herpesvirus pac-1 and pac-2 sites, respectively. The organization of the RCMV TR is unique among cytomegaloviruses with respect to the position of the pac sequences: pac-1 is located near the left end of the TR, whereas pac-2 is present near the right end. Both RCMV DNA termini carry an extension of a single nucleotide at the 3' end. Since these nucleotides are complementary, circularization of the viral genome is likely to occur via a simple ligation reaction.

Animals↗
PubMed1994

Formation of a stable complex between the human immunodeficiency virus integrase protein and viral DNA.

The integrase (IN) protein of the human immunodeficiency virus (HIV) mediates two distinct reactions: (i) specific removal of two nucleotides from the 3' ends of the viral DNA and (ii) integration of the viral DNA into target DNA. Although IN discriminates between specific (viral) DNA and nonspecific DNA in physical in vitro assays, a sequence-specific DNA-binding domain could not be identified in the protein. A nonspecific DNA-binding domain, however, was found at the C terminus of the protein. We examined the DNA-binding characteristics of HIV-1 IN, and found that a stable complex of IN and viral DNA is formed in the presence of Mn2+. The IN-viral DNA complex is resistant to challenge by an excess of competitor DNA. Stable binding of IN to the viral DNA requires that the protein contains an intact N-terminal domain and active site (in the central region of the protein), in addition to the C-terminal DNA-binding domain.

Base Sequence↗
PubMed1994

Characterization of the minimal DNA-binding domain of the HIV integrase protein.

The human immunodeficiency virus (HIV) integrase (IN) protein mediates an essential step in the retroviral lifecycle, the integration of viral DNA into human DNA. A DNA-binding domain of HIV IN has previously been identified in the C-terminal part of the protein. We tested truncated proteins of the C-terminal region of HIV-1 IN for DNA binding activity in two different assays: UV-crosslinking and southwestern blot analysis. We found that a polypeptide fragment of 50 amino acids (IN220-270) is sufficient for DNA binding. In contrast to full-length IN protein, this domain is soluble under low salt conditions. DNA binding of IN220-270 to both viral DNA and non-specific DNA occurs in an ion-independent fashion. Point mutations were introduced in 10 different amino acid residues of the DNA-binding domain of HIV-2 IN. Mutation of basic amino acid K264 results in strong reduction of DNA binding and of integrase activity.

Amino Acid Sequence↗
PubMed1994

DNA substrate requirements for different activities of the human immunodeficiency virus type 1 integrase protein.

The integrase protein (IN) of human immunodeficiency virus type 1 removes two nucleotides from both 3' ends of the viral DNA (donor cleavage) and subsequently couples the newly generated 3' OH groups to phosphates in the target DNA (integration). The sequence requirements of IN for cleavage as well as for integration of viral DNA substrates have previously been studied by mutational analyses and by adduct interference assays. We extended these studies by analysis of heteroduplex oligonucleotide substrates and by missing-base analysis. We found for some base pairs that mutation of only one of the two bases and not the other affected IN activity. These base pairs center around the cleavage site. Besides donor cleavage and integration, IN can also perform "intermolecular disintegration," which has been described as the reversal of the integration reaction. We found that this reaction is independent of viral DNA sequences. In addition, the optimum spacing between the integration sites in intermolecular disintegration does not reflect the spacing found in vivo. These results indicate that this reaction is not the exact reversal of integration but rather is a sequence-independent phosphoryl transfer reaction between gapped DNA duplex molecules.

Base Sequence↗
PubMed1994

Activities of the feline immunodeficiency virus integrase protein produced in Escherichia coli.

Retroviral DNA integration requires the activity of at least one viral protein, the integrase (IN) protein. We cloned and expressed the integrase gene of feline immunodeficiency virus (FIV) in Escherichia coli as a fusion to the malE gene and purified the IN fusion protein by affinity chromatography. The protein is active in site-specific cleavage of the viral DNA ends, DNA strand transfer, and disintegration. FIV IN has a relaxed viral DNA substrate requirement: it cleaves and integrates FIV DNA termini, human immunodeficiency virus DNA ends, and Moloney murine leukemia virus DNA ends with high efficiencies. In the cleavage reaction, IN exposes a specific phosphodiester bond near the viral DNA end to nucleophilic attack. In vitro, either H2O, glycerol, or the 3' OH group of the viral DNA terminus can serve as nucleophile in this reaction. We found that FIV IN preferentially uses the 3' OH ends of the viral DNA as nucleophile, whereas HIV IN protein preferentially uses H2O and glycerol as nucleophiles.

Amino Acid Sequence↗
PubMed1993

Identification of the catalytic and DNA-binding region of the human immunodeficiency virus type I integrase protein.

The integrase (IN) protein of the human immunodeficiency virus (HIV) is required for specific cleavage of the viral DNA termini, and subsequent integration of the viral DNA into target DNA. To identify the various domains of the IN protein we generated a series of IN deletion mutants as fusions to maltose-binding protein (MBP). The deletion mutants were tested for their ability to bind DNA, to mediate site-specific cleavage of the viral DNA ends, and to carry out integration and disintegration reactions. We found that the DNA-binding region resides between amino acids 200 and 270 of the 288-residues HIV-1 IN protein. The catalytic domain of the protein was mapped between amino acids 50 and 194. For the specific activities of IN, cleavage of the viral DNA and integration, both the DNA-binding domain and the conserved amino-terminal region of IN are required. These regions are dispensable however, for disintegration activity.

Base Sequence↗
PubMed1993

Complementation between HIV integrase proteins mutated in different domains.

HIV integrase (IN) cleaves two nucleotides off the 3' end of viral DNA and integrates viral DNA into target DNA. Previously, three functional domains in the HIV IN protein have been identified: (i) the central catalytic domain, (ii) the C-terminal DNA binding domain, and (iii) the N-terminal region, which is also necessary for activity. We have now investigated whether IN proteins mutated in different domains can complement each other. Mutant D116I does not contain an intact active site, but does bind DNA, whereas the C-terminal deletion mutant C delta 73 does not bind DNA, but does have an intact active site. Neither mutant protein mediates site-specific cleavage or integration. However, a mixture of both proteins is active, suggesting that IN functions as an oligomer, and that two subunits can have different functions; one subunit binds the (viral) DNA and another subunit provides the active site. We found three classes of mutants, corresponding to the three domains mentioned above. Mutants from different classes, but not from the same class, can complement each other. However, complementation is most efficient when the N- and C-termini are present on the same molecule.

Binding Sites↗
PubMed1993

The human immunodeficiency virus integrase protein.

The DNA integration step in the replication cycle of the human immunodeficiency virus (HIV) has been recognized as an important target in antiviral strategies. There are two main reasons for this. First, integration of HIV DNA into the human genome is required for replication of this retrovirus. Second, since the integration reaction does not have an obvious cellular counterpart, drugs that specifically inhibit integration may not be toxic for the cell. Here, we focus on the only protein known to be required for retroviral integration, the integrase (IN) protein.

DNA Nucleotidyltransferases↗
PubMed1991

Site-specific hydrolysis and alcoholysis of human immunodeficiency virus DNA termini mediated by the viral integrase protein.

Before integration of the human immunodeficiency virus (HIV) DNA, two nucleotides are removed from the 3' ends of the viral DNA by the integrase (IN) protein. We studied the chemistry of this reaction, and found that IN mediates site-specific hydrolysis of a phosphodiester bond, resulting in release of a dinucleotide. A class of alcohols (including glycerol, 1,2-propanediol, but not 1,3-propanediol) can also act as nucleophile in this reaction, and likewise the alcoholic amino acids L-serine and L-threonine can be covalently linked to the dinucleotide. No evidence was found for a covalent linkage between the IN protein and this dinucleotide, suggesting that IN directs a single nucleophilic attack of water at the specific phosphodiester bond.

Avian Sarcoma Viruses↗
PubMed1991

DNA binding properties of the integrase proteins of human immunodeficiency viruses types 1 and 2.

Integration of retroviral DNA into the host chromosome requires the integrase protein (IN). We overexpressed the IN proteins of human immunodeficiency viruses types 1 and 2 (HIV-1 and HIV-2) in E. coli and purified them. Both proteins were found to specifically cut two nucleotides off the ends of linear viral DNA, and to integrate viral DNA into target DNA. This demonstrates that HIV IN is the only protein required for integration of HIV DNA. Although the two types of IN proteins have only 53% amino acid sequence similarity, they act with equal efficiency on both type 1 and type 2 viral DNA. Binding of IN to DNA was tested: purified IN does not bind very specifically to viral DNA ends. Nevertheless, only viral DNA ends are cleaved and integrated. We interpret this as follows: in vitro quick aspecific binding to DNA is followed by slow specific cutting and integration. IN can not find viral DNA ends in the presence of an excess of aspecific DNA; in vivo this is not required since the IN protein is in constant proximity of viral DNA in the viral core particle.

Base Sequence↗
PubMed1991

Human immunodeficiency virus integrase protein requires a subterminal position of its viral DNA recognition sequence for efficient cleavage.

Retroviral integration requires cis-acting sequences at the termini of linear double-stranded viral DNA and a product of the retroviral pol gene, the integrase protein (IN). IN is required and sufficient for generation of recessed 3' termini of the viral DNA (the first step in proviral integration) and for integration of the recessed DNA species in vitro. Human immunodeficiency virus type 1 (HIV-1) IN, expressed in Escherichia coli, was purified to near homogeneity. The substrate sequence requirements for specific cleavage and integration of retroviral DNA were studied in a physical assay, using purified IN and short duplex oligonucleotides that correspond to the termini of HIV DNA. A few point mutations around the IN cleavage site substantially reduced cleavage; most other mutations did not have a drastic effect, suggesting that the sequence requirements are limited. The terminal 15 bp of the retroviral DNA were demonstrated to be sufficient for recognition by IN. Efficient specific cutting of the retroviral DNA by IN required that the cleavage site, the phosphodiester bond at the 3' side of a conserved CA-3' dinucleotide, be located two nucleotides away from the end of the viral DNA; however, low-efficiency cutting was observed when the cleavage site was located one, three, four, or five nucleotides away from the terminus of the double-stranded viral DNA. Increased cleavage by IN was detected when the nucleotides 3' of the CA-3' dinucleotide were present as single-stranded DNA. IN was found to have a strong preference for promoting integration into double-stranded rather than single-stranded DNA.

Base Sequence↗
PubMed1990

Integration of human immunodeficiency virus types 1 and 2 DNA in vitro by cytoplasmic extracts of Moloney murine leukemia virus-infected mouse NIH 3T3 cells.

An essential step in the life cycle of the human immunodeficiency virus (HIV) is integration of a DNA copy of the viral RNA into the genome of the infected cell. We show here that this step can be faithfully accomplished in vitro by the enzymatic machinery of another retrovirus, Moloney murine leukemia virus (MoMLV). Mini-HIV substrates, which are linearized plasmids with long terminal repeat sequences at their ends, were incubated with cytoplasmic extracts of MoMLV-infected NIH 3T3 cells and target DNA. The MoMLV integration apparatus carried out integration of the mini-HIV substrates correctly; the terminal nucleotides of the viral substrate were removed, and a 4-base-pair duplication of the target DNA flanked the inserted viral DNA (C. Shoemaker, S. P. Goff, E. Gilboa, M. Paskind, S. W. Mitra, and D. Baltimore, Proc. Natl. Acad. Sci. USA 77:3932-3936, 1980). Our experiments show that the substrate sequence requirements for integration in vitro were limited to a few nucleotides, as the similarity between HIV and MoMLV long terminal repeat ends is minimal.

Animals↗
PubMed1990

Analysis of the junctions between human immunodeficiency virus type 1 proviral DNA and human DNA.

Integrated retroviral DNA is flanked by short direct repeats of the target DNA. The length of these repeats is specific for the provirus that is integrated (H.E. Varmus, in J.A. Shapiro, ed., Mobile Genetic Elements, 1983). For the human immunodeficiency virus type I (HIV-1), the length of the direct repeats in the target DNA was shown to be 5 bp in one case (Muesing et al., Nature [London] 313:450-458, 1985) and 7 bp in another (Starcich et al., Science 227:538-540, 1985). One possible explanation for this discrepancy is that the direct repeats flanking HIV-1 proviruses are variable. To investigate this, we analyzed the junctions between HIV-1 proviral DNA and human DNA from nine individual clones. In each clone the provirus was flanked by a 5-bp direct repeat of human DNA. Analysis of the proviral clone previously described as being flanked by a 7-bp direct repeat of target DNA (Starcich et al., op. cit.) revealed that this clone was flanked by a 5-bp repeat instead. Therefore, we conclude that HIV-1 proviruses are flanked by 5-bp direct repeats of human DNA. The sequences of the 5-bp duplications from the different proviral clones do not have any apparent similarity to each other or to HIV-1 DNA.

Base Sequence↗
PubMed1978

Role of thyroid hormones in the normal and glucocorticosteroid hormone-induced evolution of carbamoyl-phosphate synthase (ammonia) activity in axolotl liver.

1. In axolotl liver, the activity of carbamoyl-phosphate synthase (ammonia), expressed per mg liver protein, decreases to a minimum at 5 months of age, then increases to a maximum at 8 months of age which is followed by a decrease again. The initial decrease between 3 and 5 months of age appears to be largely due to an increase in non-carbamoyl-phosphate synthase protein and the following increase between 5 and 8 months of age to a relative increase of carbamoyl-phosphate synthase protein. 2. Treatment of the animals with triiodothyronine causes an increase in carbamoyl-phosphate synthase activity, the extent of which is dependent upon hormone concentration and age of the animal. After 8 months of age no increase of enzyme occurs upon thyroid hormone treatment, although metamorphosis occurs. 3. Glucocorticosteroid hormones stimulate carbamoyl-phosphate synthase activity 2-to 3-fold in animals older than 6 months. However, in animals younger than 6 months, low concentrations of thyroid hormone, insufficient to induce metamorphosis, are necessary as permissive agents. 4. The stimulatory effects of high concentrations of thyroid hormones (T3) on carbamoyl-phosphate synthase appear to be mediated via a stimulatory effect on glucocorticosteroid biosynthesis. 5. The natural rise in enzyme activity between 5 and 8 months of age seems to be due to a rise in the concentration of circulating glucocorticosteroid hormones.

Aging↗