Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Integrase”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,801 records · Page 100Linked to original sources
PubMed1992

Nucleosomes, DNA-binding proteins, and DNA sequence modulate retroviral integration target site selection.

Integration of retroviral DNA can serve as a paradigm for cellular functions that are affected by the packaging of DNA into chromatin. We have used a novel polymerase chain reaction-based assay to survey DNA and chromatin for the precise distribution of many integration sites. Integration into naked DNA targets is non-uniform, implying a nucleotide sequence bias. In chromatin, integration occurs preferentially at positions where the major groove is on the exposed face of the nucleosomal DNA helix, generating a 10 bp periodic spacing of preferred sites. Chromatin assembly enhances the reactivity of many sites, so that integration occurs most frequently at sites in nucleosomal, rather than nucleosome-free, regions of minichromosomes. In contrast, integration is prevented in a region occupied by a site-specific DNA-binding protein. Comparisons of integration events mediated by viral nucleoprotein complexes or by two different retroviral integrases show that the integration machinery also affects target site selection.

Base Sequence↗
PubMed1994

Molecular mechanism of retroviral DNA integration.

The integration of retroviral DNA appears to be obligatory for the efficient replication of retroviruses in their respective host cells. During a natural infection, integration takes place in a process that includes biochemically and temporally discrete steps. These are: (1) the removal of two nucleotides from the 3' ends of newly synthesized linear viral DNA in the host cell cytoplasm; (2) transport of the trimmed viral DNA to the nucleus within a viral protein/DNA complex; and (3) insertion of the viral DNA into host cell DNA via a concerted cleavage and ligation reaction. The cleavage of viral DNA and its subsequent joining to host DNA are catalyzed by the retroviral enzyme, integrase (IN). Elucidation of the mechanistic details of these catalytic activities of IN has relied heavily upon the use of relatively simple in vitro assays which recapitulate the in vivo reactions. These assays and the information derived from them should also facilitate the search for potential inhibitors of IN with the ultimate goal of providing a means to halt retroviral infections, such as that which causes the acquired immunodeficiency syndrome (AIDS), effectively.

Amino Acid Sequence↗
PubMed1995

Reactivity of five anti-HIV-1 subtype O specimens with six different anti-HIV screening ELISAs and three immunoblots.

Five anti-subtype O specimens were tested by anti-HIV-1/2 screening and confirmatory assays. They can be divided into three specimens, reactive with all ELISAs, independent of the nature of the antigen (recombinant proteins or peptides) and test configuration (indirect ELISA or double antigen/sandwich ELISA). One specimen was not detected by one peptide based ELISA. One specimen was only recognized by two ELISAs and should be considered as a marker sample for the weakness of currently used ELISAs with anti-subtype O. Three different immunoblot assays available commercially detected two of the specimens with a major binding of gp160 and other viral bands, especially the integrase and reverse transcriptase. Another two specimens lacked reactivity with glycoproteins almost completely, but showed some staining with the enzymes of HIV, and would most probably be interpreted as indeterminate. The fifth specimen, which was also missed by most of the ELISAs, had very faint staining of the gp160 and a very weak staining of p24, and would most probably be interpreted as negative. Adaption of currently available tests to anti-subtype O is needed for the future reliability of anti-HIV diagnostic reagents.

AIDS Serodiagnosis↗
PubMed1993

Stable integration and expression of the Plasmodium falciparum circumsporozoite protein coding sequence in mycobacteria.

The DNA coding for the circumsporozoite protein of Plasmodium falciparum (CSP; aa 1-412) has been placed under the control of the mycobacterial promoter derived from the gene encoding the 64-kDa antigen of Mycobacterium bovis-BCG. This expression cassette was cloned into pJRD184, an Escherichia coli multicloning site vector, together with the kanamycin resistance gene from Tn903 and the attachment site and integrase gene from the temperate mycobacteriophage FRAT1. One of the resulting plasmids, pNIV2173, introduced by electroporation into both Mycobacterium smegmatis and M. bovis-BCG, integrated at a specific site in the genome of each recipient. Recombinants expressed immunoreactive polypeptides, ranging in size from 62 to 43 kDa, at a level of about 1% of total soluble proteins. Part of this material was present in the culture medium indicating that mycobacterial recombinants were able to secrete the CSP. The M. smegmatis and M. bovis-BCG recombinants, transformed with pNIV2173 and grown in absence of antibiotic, were followed for more than 400 and 50 generations respectively. Over this time span, neither DNA rearrangement nor loss of expression was observed. Inoculation of the recombinant BCG to mice did not induce humoral response to CSP nor proliferative response to CSP Th2R CD4+ T lymphocyte epitope.

Animals↗
PubMed1996

Plasmids containing cos ends inhibit the replication of phage phi CTX in Pseudomonas aeruginosa.

In bacteriophage phi CTX, the cohesive end sequences cos, the integrase gene int, the attachment site attP (the target site for int) and the gene ctx encoding a pore-forming cytotoxin CTX, are clustered. Phi CTX can infect some Pseudomonas aeruginosa strains with a subsequent induction of CTX expression. The 41 and 477 bp fragments containing cos ends of phi CTX DNA were cloned into the high copy number plasmid pHA10. After pretransformation with the cos ends containing plasmids, plaque formation of phi CTX and cytotoxin production in phi CTX-infected Pseudomonas aeruginosa cells decreased by 100- and 10-fold respectively. Twelve hours after phi CTX infection proteins binding with cooperativity to cos sequence containing cleavable ends and the 10 bp flanking sequences were detected by gel electrophoretic mobility retardation of [32P]cos DNA. The results suggest that the cos binding proteins of phi CTX are involved in phi CTX replication.

Base Sequence↗
PubMed1993

The polypurine tract, PPT, of HIV as target for antisense and triple-helix-forming oligonucleotides.

Replication of retroviral RNA into double-stranded DNA provirus involves initiation of plus-strand DNA synthesis at the polypurine tract, PPT, by the reverse transcriptase (RT). The PPT is highly conserved among the known HIV-1 retroviral isolates. It occurs twice, once within the coding region of the integrase and the other one adjacent to the 3' LTR. The data presented show that two antisense oligonucleotides, a 20-mer and a 40-mer, complementary to the PPT induce complete blocks of DNA synthesis whereas an antisense oligonucleotide outside the PPT is only slightly inhibitory. Previously polypurine sequences have been used by several groups for triplex-formation. During replication the HIV-polypurine tract, PPT, is present in a RNA-DNA hybrid. Therefore triple-helix formation consisting of RNA-DNA and a third DNA strand covering the PPT region was tested here by protection against RNase H cleavage in vitro. Incubation with a pyrimidine oligonucleotide in parallel orientation to the PPT-RNA shows some protection. GT-pyrimidine-purine mixed oligonucleotides (25-mer) led to protection against RNase H up to 50% independent of their orientation. The data suggest that triple-helix formation may have taken place with the PPT in vitro. Therefore, this highly conserved structure may prove useful in nucleic acid based anti-viral therapy with antisense or triple-helix approaches. Furthermore, the influence of HIV-1 nucleocapsid (NC) protein, NCp15, on reverse transcription is reported. The data show a two- to three-fold stimulatory effect of the NCp15 on RNA directed DNA synthesis.

Base Sequence↗
PubMed1987

Mutants of murine leukemia viruses and retroviral replication.

The analysis of retroviral mutants has played a critical role in the development of our understanding of the complex viral life cycle. The most fundamental result of that analysis has been the definition of the replication functions encoded by the viruses. From a biochemical examination of a particular step in the life cycle it is difficult to determine, for example, whether that step is catalyzed by a viral or a host enzyme; but the isolation of a viral mutant defective in that step can firmly establish that a viral function is involved. In this way many facts about the viruses have been established. We know that reverse transcriptase is encoded by the virus; that RNAase H and DNA polymerase activities reside on the same gene product; that processing of many precursor proteins is mediated by a viral proteinase; and that establishment of the integrated provirus requires a viral protein. The list of functions mediated by viral enzymes has largely been defined by the mutants isolated and studied in various laboratories. The second significant result of the studies of viral mutants has been the assignation of the replication functions to particular viral genes, and then more specifically to particular domains of these genes. Mutants and viral variants have been essential in the determination, for example, that the gag protein is the critical gene product for the assembly of a virion particle; that the env protein is the determinant of species specificity of infection; or that the LTR is a major determinant of tissue tropism and leukemogenicity. The subdivisions of functions within a given gene have similarly hinged on mutants. Genetic mapping was needed to establish that P30 is the most important region for assembly; that the proteinase and integrase functions reside, respectively, in the 5' and 3' portions of the pol gene; and that the glycosylated gag protein is dispensable for replication. A third important area of knowledge has depended heavily on viral mutants: the determination of host functions and proteins that interact with viral proteins. Variant viruses with altered or restricted host ranges serve to define differences between pairs of different host cells, and the mapping of the viral mutations serves to define the viral protein important in that interaction with the host. These studies are only in their infancy, but it is clear that substantial efforts will be made to further analyze these host functions.(ABSTRACT TRUNCATED AT 400 WORDS)

Genes, Viral↗
PubMed1982

Phasmids: hybrids between ColE1 plasmids and E. coli bacteriophage lambda.

Plasmids carrying cloned lambda att sites may be integrated into the bacteriophage genome by the site-specific recombination mechanism of lambda. The cross, referred to as "lifting" the plasmid, requires mixed infection of an Escherichia coli strain carrying the plasmid with two appropriately constructed "lifting" lambda phages. One phage donates a short left arm and the other donates a short right arm. These two short arms are of insufficient length to produce a viable phage genome and yield no recombinants when crossed on standard bacteria. However, viable recombinants are obtained when the genome length is extended by integration of one or more plasmids. We call these recombinants phasmids. They contain multiple att sites introduced at the ends of the integrated plasmids, and in the presence of integrase, recombination between these att sites can be exploited to effect release of the plasmid components. These novel genetic elements can be used in a variety of ways as vectors in genetic manipulation experiments. Sequences cloned in phasmids may be studied as a component of either a plasmid and or of a phage, and easily interconverted between the two states.

Attachment Sites, Microbiological↗
PubMed1993

Sequence analysis of closely related retrotransposon families from fission yeast.

Two families of retrotransposons, Tf1 and Tf2, have been isolated from the fission yeast, Schizosaccharomyces pombe. We report here the nucleotide (nt) sequence of a Tf2 element, the only retrotransposon family known from the commonly used laboratory strains, 972 and 975, and their derivatives. The total nt sequence of Tf2 was derived from the complete sequence of the coding region and 3' long terminal repeat (LTR) of randomly cloned element Tf2-1, and from a full 5' LTR and approximately one-third of the open reading frame (ORF) of Tf2-43, a Tf2 element found in the head-to-head orientation adjacent to the Sz. pombe rpb6 gene. The two Tf2 sequences are nearly identical and both of them contain a single ORF encoding a protein with regions of sequence similar to protease, reverse transcriptase, RNase H (RH) and integrase from other retrotransposons and retroviruses. Sequence comparisons between Tf1 and Tf2 indicate an extreme divergence of the putative capsid protein-encoding regions of these two elements, as well as divergence of a segment of the LTR, but otherwise virtually identical sequence.

Amino Acid Sequence↗
PubMed1995

A transposon-like sequence adjacent to the AccI restriction-modification operon.

We have cloned and sequenced the accIRM genes from Weeksella zoohelcum (the original identification of this strain as Acinetobacter calcoaceticus was incorrect). Our sequence differs in the coding regions from a previously published sequence by the addition of three nucleotides near the 3' end of the DNA methyltransferase-encoding gene (accIM). We have sequenced approx. 3 kb beyond this operon. Two genes were found, convergently transcribed with the R-M operon. The first of these genes encodes a protein which shows significant similarity to the recombinases of the phage integrase family. The W. zoohelcum recombinase may function as a transposon resolvase, as in Tn4430. The recombinase-encoding gene is followed by a putative transposase (Tnp), which is in turn followed by a terminator which is predicted to be Rho-dependent for the recombinase-Tnp operon and Rho-independent for the convergent R-M operon. Since the G + C content of the two operons is notably different, it is possible that the terminator is at the extremity of the mobile element and serves to protect it from incoming transcription.

Amino Acid Sequence↗
PubMed1994

Sequence analysis of a unique temperature phage: mycoplasma virus L2.

Mycoplasma virus L2 is a quasi-spherical enveloped virion containing circular double-stranded DNA. L2 infection of Acholeplasma laidlawii host cells leads to a noncytocidal productive infection cycle followed by establishment of lysogeny in all (or most) infected cells, with viral DNA integrated into the host cell genome. The L2 genome has been sequenced and analyzed. L2 DNA is 11,965-bp long and contains 15 open reading frames (ORFs). One of these, ORF13*, has its start codon within and in the same reading frame as ORF13. The ORFs are clustered in four groups separated by noncoding intergenic regions, suggesting that gene expression involves transcription of genes in a cluster into polycistronic mRNA and translation of these genes via translational coupling or reinitiation. Fifteen L2 start codon sites have been defined and resemble those of eubacteria. The N-terminal sequences of two ORFs appear to be signal peptides, and the gene product of one of these may be an L2 virion integral membrane protein. The ORF 5 product has been tentatively identified as an integrase, based on its sequence similarity to site-specific recombinases. The putative attP integration site has been mapped to an intergenic region, 280-bp downstream from ORF 5. Two putative DNA replication ori sites have been mapped. Each is in an intergenic region and contains a DnaA-box bounded by A + T-rich 6-mer repeats.

Acholeplasma laidlawii↗
PubMed1994

In-frame linker insertion mutagenesis of yeast transposon Ty1: phenotypic analysis.

A plasmid bearing a transpositionally functional GAL1::Ty1 fusion was mutagenized by insertion of four or five codons semirandomly throughout the plasmid. This collection of mutant plasmids was introduced into yeast cells and studied with regard to the properties of the mutant Ty1-encoded proteins and the transposition phenotypes observed. All of the transposition-inactivating mutations were previously found to be recessive with the exception of a single mutation in TYA. In this mutant, TYA protein of normal abundance is produced, but the virus-like particles containing this protein are unstable and have aberrant behavior. The effects of mutations in noncoding regions, as well as the capsid protein coding region TYA, and the regions encoding the protease, integrase and reverse transcriptase proteins are described. Effects on gene expression, types of proteins produced, proteolysis of precursor proteins, virus-like particle structure, and biochemical activities of the encoded proteins are summarized. In addition, we show that one of the mutations in the 3' LTR represents a new nonessential site into which foreign marker DNA can be inserted without compromising transposition.

Codon↗
PubMed1995

Characterization of an open reading frame involved in site-specific integration of filamentous phage Cf1t from Xanthomonas campestris pv. citri.

Cf1t is a single-stranded DNA filamentous phage; a 1.9-kb segment of DNA from Cf1t was found to be responsible for site-specific integration into Xanthomonas campestris pv. citri (XW47), in the absence of any Xanthomonas origin of replication. Deletion analysis and introduction of amber stop codons into this fragment from Cf1t revealed an open reading frame (ORF344) which was involved in the integration function. The predicted amino-acid sequence of ORF344 bears no homology with conserved sequences of the integrase family.

Amino Acid Sequence↗
PubMed1995

Anti-HIV and anti-tumor activities of recombinant MAP30 from bitter melon.

MAP30 is an anti-HIV plant protein that we have identified and purified to homogeneity from bitter melon (Momordica charantia). It is capable of acting against multiple stages of the viral life cycle, on acute infection as well as replication in chronically infected cells. In addition to antiviral action, MAP30 also possesses anti-tumor activity, topological inactivation of viral DNA, inhibition of viral integrase and cell-free ribosome-inactivation activities. We have cloned and expressed the MAP30 gene. The objective of this study is to characterize recombinant MAP30 (re-MAP30) and to determine its anti-HIV, anti-tumor and other activities. We report here that re-MAP30 inhibits HIV-1 and certain human tumors to the same extent as its native counterpart, natural MAP30 (nMAP30). The anti-HIV activity was measured by quantitative focal syncytium formation on CEM-ss cell monolayers, viral core protein p24 expression and viral-associated reverse transcriptase activity in HIV-1-infected H9 cells. The anti-tumor activity was measured by metabolic labeling of protein synthesis in tumor cells. In the dose range of the assay, re-MAP30 exhibits little toxicity to the uninfected viral target cells and other normal human cells. Identical to nMAP30, re-MAP30 is also active in topological inactivation of viral DNA, inhibition of viral DNA integration and cell-free ribosome inactivation. The cloning and expression of the gene encoding biologically active re-MAP30 provides an abundant source of homogeneous material for clinical investigations, as well as structure-function studies of this novel antiviral and anti-tumor agent.

Amino Acid Sequence↗
PubMed1995

Selection of species-specific DNA probes which detect strain restriction polymorphism in four Bifidobacterium species.

Randomly cloned fragments (in a size range 1 to 2.5 kb) of DNA from Bifidobacterium longum ATCC 15707, B. adolescentis CIP 64.59T, B. bifidum CIP 64.65 and B. animalis ATCC 25527 were used as hybridization probes to characterize strains of these species and distinguish them from closely related Bifidobacterium species. The fragments were screened for hybridization with native DNA from 41 different Bifidobacterium strains. For each species, a fragment hybridizing specifically with DNA from strains of the same species was isolated. Each fragment was then hybridized with restriction digests in order to study the genome polymorphism. In some of the tested B. longum strains including strain ATCC 15707, the species-specific fragment L6/45 hybridized with 2 fragments instead of one as expected. Sequence of the fragment revealed the presence of an ORF which had an amino acid sequence similar to the site-specific recombinases of lambda integrase family. Moreover, Southern analysis demonstrated that at least 3 copies of this fragment are present in the chromosome of B. longum ATCC 15707 and in some other B. longum strains. The species-specific fragment A6/17 of B. adolescentis hybridized with the same restriction fragment on the eight strains of this species tested. The B. bifidum-specific fragment hybridized with different DNA restriction fragments according to the strain. The restriction fragment an1 from B. animalis ATCC 25527 hybridized with the same restriction fragment from strain B. animalis ATCC 27536. However, these two strains could be differentiated by another restriction pattern. Thus, hybridization results highlight the genetic polymorphism which exists among Bifidobacterium strains of the same species.

Base Sequence↗
PubMed1995

Innovative approaches to gene therapy.

The past year has witnessed several advances in the development of targeted, cell-specific gene delivery systems of both viral and non-viral origin. Progress has been made in understanding the cellular mechanisms of nuclear import, and novel sequence-specific integrases have been developed that mediate insertion of DNA molecules into specific target sequences. Knowledge of the mechanisms by which herpes simplex virus and Epstein-Barr virus escape from immune surveillance has also advanced significantly; this may be exploited to reduce the immunogenicity of certain therapeutic gene products.

Animals↗
PubMed2005

Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis.

RNase H belongs to a nucleotidyl-transferase superfamily, which includes transposase, retroviral integrase, Holliday junction resolvase, and RISC nuclease Argonaute. We report the crystal structures of RNase H complexed with an RNA/DNA hybrid and a mechanism for substrate recognition and two-metal-ion-dependent catalysis. RNase H specifically recognizes the A form RNA strand and the B form DNA strand. Structure comparisons lead us to predict the catalytic residues of Argonaute and conclude that two-metal-ion catalysis is a general feature of the superfamily. In nucleases, the two metal ions are asymmetrically coordinated and have distinct roles in activating the nucleophile and stabilizing the transition state. In transposases, they are symmetrically coordinated and exchange roles to alternately activate a water and a 3'-OH for successive strand cleavage and transfer by a ping-pong mechanism.

Arabidopsis Proteins↗
PubMed2004

Ini1/hSNF5 is dispensable for retrovirus-induced cytoplasmic accumulation of PML and does not interfere with integration.

Retroviral infection triggers the cytoplasmic translocation of two Crm1-dependent shuttle factors, namely the Ini1 (integrase interactor 1, hSNF5) and the promyelocytic leukemia (PML) protein. Blocking nuclear export of shuttle factors by leptomycin B increases the efficiency of retroviral integration, suggesting that some may mediate antiviral activity. While PML was shown to counteract proviral establishment, it remained unclear whether Ini1, a protein implicated in various processes during human immunodeficiency virus replication, has the same potential. Employing RNA interference-mediated knock-down of Ini1, we show here that the simultaneous accumulation of both proteins in the cytoplasm likely reflects two non-interdependent phenomena. Furthermore, Ini1 does not interfere with retroviral integration, as cells lacking Ini1 show no increased infection susceptibility.

Annexin A5↗

Refine your search to explore more results.