Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “inverted terminal repeat”

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 559 records · Page 31Linked to original sources
PubMed1990

A recombinant fowlpox virus expressing the hemagglutinin-neuraminidase gene of Newcastle disease virus (NDV) protects chickens against challenge by NDV.

The hemagglutinin-neuraminidase (HN) gene from the Beaudette C strain of Newcastle disease virus (NDV) has been expressed in a recombinant fowlpox virus vector. The HN gene, under the control of the vaccinia p7.5 promoter, was inserted into a nonessential gene in the terminal inverted repeats of fowlpox virus. Expression was demonstrated in tissue culture, a protein of the correct size for fully glycosylated HN protein being recognized by an HN-specific monoclonal antibody on Western blots. When the recombinant fowlpox virus was inoculated into chickens by intravenous or wing-web routes, antibody which recognizes HN from purified NDV virions was produced. Protective immunity to NDV was generated in the chickens; at the highest dose of vaccine 100% of the chickens tested were protected against challenge with a virulent strain of NDV.

Animals↗
PubMed1991

Deletion of 55 open reading frames from the termini of vaccinia virus.

Each copy of the inverted terminal repeat of vaccinia virus consists of 8 kb of DNA containing 9 ORFS flanked near the terminus of the genome by 4 kb of repetitive DNA which in turn contains blocks of tandem repeats. Using plasmids containing repetitive DNA as the external arm, we have generated deletions at both the left and the right termini of the vaccinia genome. We report here the engineered deletion within a single vaccinia virus of 32.7 kb of DNA (including 38 ORFS) from the left terminus and 14.9 kb of DNA (including 17 ORFS) from the right terminus.

Base Sequence↗
PubMed1992

The densovirus of Junonia coenia (Jc DNV) as an insect cell expression vector.

An infectious genome of the Junonia coenia densovirus (Jc DNV) has been recently cloned and sequenced. We investigated the ability of this cloned genome to be used as expression vector by inserting the lacZ gene of Escherichia coli as fusion gene in the major open reading frame (ORF 1) of the viral sequence. The resulting recombinant plasmid designated pBRJlac Z was transfected into insect SPC-SL 52 cells and the expression of beta-galactosidase (beta-gal) was detected qualitatively or quantitatively by using Xgal or ONPG as chromogenic substrates. Western blot analysis revealed that beta-gal was expressed as chimeric capsid-beta-gal polypeptides. This provided evidence that ORF1 codes for structural polypeptides which share a common C-terminal sequence. Construction of plasmids with alterations or deletions in ORF2, 3 or 4, allowed us to implicate nonstructural (NS) functions in viral DNA replication. Deletions in inverted terminal repeats or in NS functions did not abolish expression of capsid polypeptides but reduced it dramatically. Encapsidation of Jlac Z recombinant genome was achieved by trans-complementation with plasmids bearing intact structural and nonstructural functions. Detection of a beta-gal activity in SPC-SL 52 cells following several subcultures post-transfection suggests that Jlac Z recombinant genome could be maintained in an integrative or episomal state.

Animals↗
PubMed1992

Complete nucleotide sequence of the cloned infectious genome of Junonia coenia densovirus reveals an organization unique among parvoviruses.

We previously constructed a recombinant plasmid, pBRJ, encompassing an infectious Junonia coenia densovirus (JcDNV) genome (M. Jourdan et al. (1990). Virology 179, 403-409). We report here the complete viral sequence of pBRJ. The genome, 5908 nucleotides (nt) long, consists of an internal unique sequence flanked by long (517 nt) inverted terminal repeats. The first 96 bases of one extremity can fold into a typical Y-shaped hairpin structure. The opposite extremity is incomplete, lacking 88 nt. These terminal structures, similar to those of dependoviruses, human parvovirus B19 and Bombyx mori densovirus (BmDNV), strongly suggest a common mechanism of DNA replication for these parvoviruses. JcDNV genomic organization is unique among parvoviruses in that coding sequences are evenly distributed in the 5' half of both strands. On one strand, the major open reading frame (ORF1) encodes the four structural proteins. On the complementary strand, ORF2, ORF3 (included in ORF2), and ORF4 probably encode nonstructural proteins. JcDNV genome has little DNA homology with vertebrate parvoviruses and surprisingly even less with the two densoviruses presently sequenced. ORF1 contains the highly conserved PGY and G-rich regions and ORF2 the NTP-binding domain common to most structural and to all nonstructural vertebrate parvoviral ORFs, respectively. The single homology between JcDNV and BmDNV is unexpectedly located in JcDNV NTP-binding domain and BmDNV ORF2 assumed to encode structural polypeptides. Only a weak homology exists between JcDNV and Aedes DNV in their NTP-binding domain.

Amino Acid Sequence↗
PubMed1979

Biogenesis of poxviruses: mirror-image deletions in vaccinia virus DNA.

Restriction endonuclease analysis of viral DNA extracted from wild-type and temperature-sensitive mutants of vaccinia IHD-W (Dales et al., 1978) revealed sequence alterations in approximately 20% of all ts clones examined. The rearrangements were due to deletions up to 250 nucleotide pairs long. Using Eco RI, Sal I, Bam I, Hpa I and Ava I, the deletions were always observed in the same fragments, while analysis with Hind III demonstrated deletions of identical size in the two terminal fragments. Since vaccinia virus contains inverted terminal repeats of more than 10 kb, these clones possess identical deletions of opposite orientation at both ends of the genome. Analysis of several revertants of the ts mutants demonstrated that the deletions probably arise as events independent from those producing ts lesions and are generated spontaneously at high frequency. This implies that a single event during replication caused the elimination of nonessential information, and suggests that circular intermediates must exist transiently during viral replication.

Base Sequence↗
PubMed1981

The mechanism of cytoplasmic orthopoxvirus DNA replication.

Orthopoxvirus DNA replication occurs in the cytoplasm of infected cells within discrete foci designated as virosomes. We show that newly synthesized rabbit poxvirus (RPV) virosomal DNA consists predominantly of concatamers wherein unit length molecules are joined by fusion of two left (LL) or right (RR) ends, resulting in genomes aligned in alternating head-to-head and tail-to tail mirror image arrays. These concatameric molecules serve as the substrates from which unit length DNA molecules are excised during morphogenesis. We propose a mechanism by which internal deletions within these concatameric arrays prior to genome excision and packaging could create inverted terminal repeats and generate gene duplications.

Cytoplasm↗
PubMed1982

A novel type of transposon generated by insertion element IS102 present in a pSC101 derivative.

We describe a novel type of transposon in the tetracycline resistance plasmid pYM103, a derivative of pSC101 carrying a single copy of an insertion element IS102. The new transposons we found were identified as DNA segments, approximately 6 kb (Tn1021) and 10 kb (Tn1022) in length, able to mediate the cointegration of pYM103 with plasmid Col E1. The resulting cointegrate contains either of these pYM103 segments duplicated in a direct orientation at the junctions of the parent plasmids. A direct duplication of a 9 bp sequence at the target site in Col E1 is found at the junctions for cointegration. Both transposons have IS102 at one end and also contain different lengths of the pYM103 DNA adjacent to IS102, including the tetracycline resistance gene. Each transposon contains terminal inverted repeats of a short nucleotide sequence. These results and the fact that IS102 can itself mediate plasmid cointegration, giving rise to a duplication of a 9 bp target sequence, indicate that IS102 is responsible for generation of Tn1021 and Tn1022. They are quite different from the common IS-associated transposons, which are always flanked by two copies of an IS element, and may be similar to transposons such as those of the Tn3 family and phage Mu.

Bacteriocin Plasmids↗
PubMed1982

FB elements are the common basis for the instability of the wDZL and wC Drosophila mutations.

The DNA insertions that cause the highly unstable mutations wC and wDZL share extensive homology with the FB family of transposable elements. FB elements carry long, internally repetitious, inverted terminal repeats and thus differ in structure from other transposable elements. Our results suggest that FB elements may excise and cause chromosomal rearrangements at unusually high frequencies. The wC insertion is a single FB element. The wDZL insertion differs in that it contains two FB elements, one at each terminus. The wC and wDZL insertions contain 4.0 and 6.5 kilobase nonhomologous segments between their terminal repeats. In contrast to the middle repetitive FB elements, the central segment of the wDZL insertion is single-copy and present at a fixed location in the wild-type genome. It has apparently been transposed by the action of flanking FB elements, causing the wDZL mutation at its new location.

Alleles↗
PubMed1985

Mitochondrial DNA rearrangements associated with fertile revertants of S-type male-sterile maize.

The mitochondrial genome of the S-type male-sterile cytoplasm of maize appears to be a collection of linear DNA molecules that are maintained by two linear episomal DNA species, S1 (6397 bp) and S2 (5453 bp), recombining with larger circular molecules. The M825 inbred nuclear genotype promotes a high frequency of spontaneous fertile mutants. Where the mutation is maternally inherited, analysis of the mitochondrial DNA reveals that the S1 and S2 episomes and all associated linear molecules have been lost. Integrated copies of the S1 and S2 episomes are retained, though part of one of the two terminal inverted repeats of the integrated S2 sequence has been deleted in all revertants studied. This deletion appears to correlate with the absence of the S2-URF-1 transcript.

Base Sequence↗
PubMed1984

A physical and functional analysis of Tn917, a Streptococcus transposon in the Tn3 family that functions in Bacillus.

The erythromycin-resistance (Emr)-conferring transposon Tn917, first isolated in the genus Streptococcus, has in previous work been shown to function efficiently in the spore-forming species Bacillus subtilis, where it has been developed as a tool for identifying and studying sporulation genes. In the present work, a physical analysis of Tn917 was undertaken, including detailed restriction mapping, chemical DNA sequencing, heteroduplex studies, and Southern hybridization analysis, as a first step in understanding the genetic organization of this useful insertion element. The location and transcriptional orientation of the transposon-borne erm gene (the gene responsible for the Emr phenotype) have been determined, and a partial sequence of DNA 5' to the coding sequence of this gene indicates that its inducibility is probably the result of "translational attenuation," a mechanism known to be responsible for the regulation of at least two other gram-positive erm genes. Restriction mapping and heteroduplex analysis have revealed extensive homology between Tn917 and the Staphylococcus transposon Tn551, throughout virtually their entire lengths, and DNA sequencing studies have revealed a remarkably high degree of sequence correspondence within the terminal inverted repeats of Tn917, Tn551 and the gram-negative transposon Tn3. Tn917 was also shown to generate a 5-bp duplication upon insertion, as do Tn3 and Tn551 (and all of the other Tn3-related elements studied thus far), strengthening the conclusion that these three transposons are members of a highly dispersed family of related insertion elements which populate both gram-positive and gram-negative genera.

Bacillus↗
PubMed1984

Construction of a cloning site near one end of Tn917 into which foreign DNA may be inserted without affecting transposition in Bacillus subtilis or expression of the transposon-borne erm gene.

A 1.3-kb restriction fragment carrying a cat gene derived from Staphylococcus aureus was inserted by ligation in both possible orientations into a HpaI restriction site located less than 300 bp from one end of Tn917. The resulting transposon derivatives were unimpaired in their ability to make and resolve transpositions into the chromosome of Bacillus subtilis and they displayed no detectable defect in expression of the inducible erm gene carried by the transposon. This demonstrates that the HpaI site itself, and perhaps the entire 250- to 300-bp region between the HpaI site and the nearest transposon terminal inverted repeat consists of nonessential DNA, and is there fore available to be modified or used as a cloning site with the expectation that the resulting transposon derivatives should be capable of normal transposition activity. To facilitate such manipulations, the HpaI site was "replaced" by a 24-bp DNA segment which contains a BamHI site flanked on either side by SmaI sites; these BamHI and SmaI sites are unique to the transposon. Several of the plasmid constructions undertaken in the course of this work illustrate ways in which homologous recombination may be used in conjunction with ligation in B. subtilis (and other bacteria, such as Streptococcus pneumoniae, which have similar mechanisms for DNA uptake during competence) to facilitate significantly the recovery of certain kinds of recombinant molecules.

Bacillus subtilis↗
PubMed1990

Nucleotide sequence analysis of IS427 and its target sites in Agrobacterium tumefaciens T37.

We have determined the nucleotide sequence of IS427, an insertion sequence from Agrobacterium tumefaciens T37, IS427 is 1271 bp long, contains 16-bp imperfect terminal inverted repeats, and generates a 2-bp target sequence duplication. It is present at three sites in the pTiT37 plasmid and is absent from the chromosome of A. tumefaciens T37. Each of the IS427 elements sequenced was near a site with sequence homology to integration host factor (IHF)-binding sites which suggested that IHF may be involved in IS427 transposition.

Amino Acid Sequence↗
PubMed1988

Nucleotide sequence of the M segment of Germiston virus: comparison of the M gene product of several bunyaviruses.

The complete nucleotide sequence of the M RNA segment of Germiston bunyavirus was determined from plasmids containing overlapping M cDNA inserts. The M segment is 4534 nucleotides long and contains a 50-base-long inverted terminal repeat which can form a stable hydrogen-bonded secondary structure with a delta G of -45.8 kcal/mol. The RNA molecule complementary to viral RNA contains a single large open reading frame that encodes a 1437 amino acid-long protein with hydrophobic amino and carboxy terminal regions, which could represent signal and anchor sequences, respectively. It is presumed that this gene product is the polyprotein precursor to glycoproteins G1 and G2 and to the nonstructural polypeptide NSM. The nucleotide and amino acid sequences of the M RNA of Bunyamwera virus (prototype of the serogroup) and snowshow hare and La Crosse viruses (California serogroup) (Lees et al., 1986; Eshita and Bishop, 1984; Grady et al., 1987) were compared to those of Germiston virus. An overall amino acid sequence homology of 44% was found between Germiston and snowshoe hare viruses and of 61% between Germiston and Bunyamwera viruses. Most of the cysteines, three out of seven of the potential glycosylation sites, as well as the N and C terminal hydrophobic domains, are conserved between the four viruses.

Amino Acid Sequence↗
PubMed1981

The nucleotide sequence of IS5 from Escherichia coli.

A 3-kb fragment of Haemophilus haemolyticus DNA which carries the HhaII restriction (r) and modification (m) genes has been cloned into the PstI site of pBR322 (Mann et al., 1978). When propagated in Escherichia coli, it was observed that spontaneous insertions of IS5 inactivated the restriction gene, producing r- mutants at a frequency of 10(-6). Electron microscopy, restriction-site mapping and sequence analysis of two r- plasmids have demonstrated the presence of IS5 at a single target site in both possible orientations. The complete nucleotide sequence of IS5 has been determined. It is 1195 bp long and has inverted terminal repeats of 16 bp. The target site for IS5 in this plasmid is 5'-CTAG. Approx. ten copies of IS5 were found to be present at about the same locations on the E. coli chromosome in various K-12 strains, using Southern hybridization analysis.

Base Sequence↗
PubMed1983

Chloramphenicol-inducible gene expression in Bacillus subtilis.

A cloned Bacillus pumilus cat gene expresses chloramphenicol-inducible chloramphenicol acetyltransferase activity in Bacillus subtilis. The chloramphenicol inducibility trait was shown to be determined by a 234-bp region of the cloned DNA. Nucleotide sequence analysis of this 234-bp segment indicated that the cat ribosome-binding site occurs within a 40-bp region containing 14-bp terminal inverted repeat sequences. Transcription of this region into RNA should sequester the cat ribosome-binding site in a stable stem-loop conformation. Chloramphenicol-mediated destabilization of the stem-loop is suggested as the basis for the chloramphenicol inducibility phenotype.

Acetyltransferases↗
PubMed1986

Analysis of Tn3 sequences required for transposition and immunity.

Tn3 is a 5-kb transposon (Tn) with 38-bp inverted terminal repeats (ITR). The two 38-bp terminal sequences are required in cis for Tn3 transposition. In this study, the role of the ITR in Tn3 transposition has been further dissected by the use of various mini-Tn3 Tn's. The transposition frequency of these mini-Tn's demonstrate that Tn3 contains no sequence other than the ITR sequences that are necessary for the first step in transposition; the two terminal repeats must be oriented as ITR for transposition to occur; the outside 34 bp of the ITR are required for transposition; and reducing the distance between the terminal sequences does not affect transposition frequency. Moreover, mutant copies of the ITR sequences that cannot function in transposition do not confer transposition immunity.

Base Composition↗
PubMed1988

A novel vector allowing the expression of genes in a wide range of gram-negative bacteria.

The construction and use of a novel vector allowing the expression of genes in a wide range of Gram-negative bacteria is described. The vector utilizes the regulatory region from IS50. The 70-bp promoter region was isolated from one of the terminal inverted repeats of Tn5 by creating EcoRI and Sa/I or PstI restriction sites by in vitro mutagenesis. This 70-bp region was shown to direct the expression of cat and lacZ genes in different bacterial genera including Alcaligenes, Enterobacter cloacae, Klebsiella pneumoniae, Pseudomonas stutzeri, Pseudomonas fluorescens, and Serratia marcescens. Different strains containing the cat gene behind the regulatory elements of IS50 were able to tolerate high concentrations (300 micrograms/ml) of chloramphenicol in the medium. The 70-bp promoter region was cloned into a broad-host-range plasmid behind multiple cloning sites to create pAV10, which has unique restriction sites for BamHI, KpnI, SstI, and XbaI. Genes cloned into pAV10 can be expressed in a variety of Gram-negative bacteria.

DNA Transposable Elements↗
PubMed1989

IS257 from Staphylococcus aureus: member of an insertion sequence superfamily prevalent among gram-positive and gram-negative bacteria.

The nucleotide sequences for the IS257 family of insertion sequences from Staphylococcus aureus were compared with those of the ISS1 family from Streptococcus lactis and the IS15 family which is widespread amongst Gram-negative bacteria. These elements have a striking degree of similarity in both their putative transposase polypeptide sequences and their nucleotide sequences (40 to 64% between pairs), including 12 out of 14 bp conservation in their terminal inverted repeats. The evolutionary distance between the IS15 family and the IS257 and ISS1 families of Gram-positive origin is approximately twice that between the IS257 and ISS1 families. Analysis of base substitutions in the three sequences has provided insights into the effect of selection for the G + C content of immigrant genes to conform to that of their hosts, and into the evolution of biases in overall amino acid composition of cellular proteins in prokaryotes and eukaryotes. The IS257, ISS1, IS15 families form a superfamily of insertion sequences that has been involved in the spread of a number of antimicrobial resistance determinants in Gram-positive and Gram-negative pathogens.

Amino Acid Sequence↗