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At least 109 records · Page 6Linked to original sources
PubMed2001

Four new inverted terminal repeat sequences from bovine adenoviruses reveal striking differences in the length and content of the ITRs.

The inverted terminal repeat (ITR) of the genome of four bovine adenovirus (BAdV) types have been sequenced, analysed and compared to the ITRs of other adenoviruses. The length of ITRs of the examined BAdVs ranged between 59 and 368 base pairs, thus the presently known longest adenovirus ITR sequence is from BAdV-10. The conserved motifs and characteristic sequence elements of the ITRs providing different binding sites for replicative proteins of viral and cellular origin seemed to be distributed according to the proposed genus classification of BAdVs. The ITRs of BAdV-10 share similarity with the members of the genus Mastadenovirus, while the ITRs of the other three sequenced serotypes (BAdV-4, 5 and strain Rus) which are candidate members of the genus Atadenovirus are very short and contain NFI and Sp1 binding sites only. The analysis of the new ITRs implied that the nucleotide sequence of the so-called core origin is highly preserved within the mastadenovirus genus only.

Adenovirus E2 Proteins↗
PubMed1985

Isolation of novel herpes simplex virus type 1 derivatives with tandem duplications of DNA sequences encoding immediate-early mRNA-5 and an origin of replication.

Two naturally occurring variations of herpes simplex virus type 1 (Patton strain) with novel tandem DNA sequence duplications in the S component were isolated, and the DNA was characterized. These variants were identified among a number of plaque isolates by the appearance of new restriction enzyme fragments that hybridized with radiolabeled DNA from the BamHI Z fragment (map coordinates 0.936 to 0.949) located in the unique S region. One isolate, SP26-3, carried a 3.1-kilobase-pair duplication defined by recombination between a site in the BamHI Z fragment and a site near the origin of replication in the inverted repeat sequence of the S component carried by the EcoRI H fragment. The other isolate, SP22-4, carried a 3.5-kilobase-pair duplication defined by a recombination event between a tandem repeat array in the BamHI Z fragment and a site near the amino terminus of the Vmw175 gene in the S-region inverted repeat sequence contained in the EcoRI K fragment. Both duplicated segments contained the entire immediate early mRNA-5 coding region as well as the origin of replication located in the inverted repeat sequence of the S component. The DNA sequence of each duplication joint was determined.

Base Sequence↗
PubMed1980

Inverted terminal repeat sequence in the macronuclear DNA of Stylonychia pustulata.

The structure of macronuclear DNA of a hypotrichous ciliate, Stylonychia pustulata, was examined by both electron microscopy and nucleotide sequence analysis. The DNA in the macronucleus consists of small linear molecules with average length of about 3400 base pairs (bp). Most, if not all, of these DNA molecules have identical inverted terminal repeat sequence of 20 nucleotide residues. This sequence is 5'-CCCCAAAACCCC-AAAACCCC.

Animals↗
PubMed1997

Analysis of DNA inversions in the shufflon of plasmid R64.

The shufflon, a multiple DNA inversion system in the plasmid R64, consists of four DNA segments flanked and separated by seven 19-bp repeat sequences. Site-specific recombinations mediated by the rci product occur between each inverted repeat sequence, resulting in inversions of the four segments independently or in groups. The seven 19-bp repeat sequences are classified into four types (repeat-a, -b, -c, and -d), according to their 3-bp variable sequences. We individually cloned A, B, and C segments of the R64 shufflon and determined the in vivo inversion frequency of each segment. The inversion frequencies of three segments differed greatly. The inversion frequency declined in the following order: segments A, B, and C. Synthetic 19-mer oligonucleotides corresponding to both strands of repeat-a, -b, -c, and -d sequences were inserted into appropriate sites of pBR322. The rci-mediated DNA inversion occurred between two synthetic inverted repeats, indicating that the 19-bp inverted repeat sequences are the sole elements required in cis for the shufflon system. The inversion frequencies of DNA segments flanked by various sequences indicate that the four types of repeat sequences determine the inversion frequency of the four DNA segments of the R64 shufflon. Deletion of a DNA segment flanked by direct repeat sequences could not be detected.

DNA Nucleotidyltransferases↗
PubMed1987

Specific binding of transposase to terminal inverted repeats of transposable element Tn3.

Tn3 transposase, which is required for transposition of Tn3, has been purified by a low-ionic-strength-precipitation method. Using a nitrocellulose filter binding assay, we have shown that transposase binds to any restriction fragment. However, binding of the transposase to specific fragments containing the terminal inverted repeat sequences of Tn3 can be demonstrated by treatment of transposase-DNA complexes with heparin, which effectively removes the transposase bound to the other nonspecific fragments at pH 5-6. DNase I "footprinting" analysis showed that the transposase protects an inner 25-base-pair region of the 38-base-pair terminal inverted repeat sequence of Tn3. This protection is not dependent on pH. Interestingly, binding of the transposase to the inverted repeat sequences facilitates DNase I to nick at the end of the Tn3 sequence. It was also observed that the transposase protects the end regions of restriction fragments with a cohesive sequence at their 5' end or with a flush end from DNase I cleavage. The specific and nonspecific binding of transposase to DNA is ATP-independent.

Adenosine Triphosphate↗
PubMed1990

Evidence of introduction by molecular cloning of artificial inverted sequence at the 5' terminus of the sense strand of rat insulin-like growth factor-I cDNA.

A cDNA of insulin-like growth factor (IGF)-I mRNA was obtained from a rat liver cDNA library. This cDNA contained a 5' terminal sequence of 48 base pairs complementary to a sequence in the 3' terminal region (an inverted repeat sequence) except for one nucleotide insertion in the 3' region. Base sequence analysis of this cDNA, northern blot analysis of rat liver mRNA using a probe specific to 5' region of cDNA, base sequence studies of the 5' upstream region of a clone of the rat IGF-I gene, and some other studies suggested strongly that the inverted repeat sequence of the IGF-I cDNA used was introduced artificially during preparation of the cDNA library.

Amino Acid Sequence↗
PubMed1986

DNA inversion in bacteriophage Mu: characterization of the inversion site.

Gin-mediated site-specific recombination promotes inversion of the G segment of phage Mu. The crossover takes place between two 34 bp-long inverted repeat sequences flanking the G segment. We have characterized the inversion site, the target for the site-specific recombination mechanism. An artificial invertible segment was constructed which consists of parts of the invertible segments of Mu and phage P1, which in this respect are largely homologous. Upon inversion of this hybrid segment the crossover site could be located, by DNA sequencing, in the ACCT sequence of the centre of symmetry in the inverted repeat in Mu. The hybrid Mu-P1 segment inverts at a lower frequency than its parental invertible segments probably because of the mismatches between the inverted repeats of Mu and P1. This suggests that base pairing between the inverted repeats is an intermediate step in recombination. Plasmids with subcloned G segments lacking the adjacent beta region of Mu or the corresponding region in P7, a relative of P1, are deficient in inversion. By analysis through site-specific mutagenesis of Mu DNA, an enhancer element with multiple recognition sites was identified which is necessary for efficient inversion. This component of the inversion site was located in a 170 bp segment within the Mu beta region, 30 bp to the right of the inverted repeat sequence, but can be separated from the crossover site by a 1200 bp insertion without losing its effect.

Bacteriophage mu↗
PubMed1978

Evidence for translocation of DNA sequences during sea urchin embryogenesis.

Hairpin-like DNA was prepared in vitro from the family of sequences that are inverted relative to each other and, as pairs, are relatively homologous and adjacent on the sea urchin genome. The majority of these hairpins are shown to have base pair mismatch positions distributed along their stems. Comparison of the hairpins derived from the DNA of morula, blastula, and gastrula stage embryos shows that during embryogenesis there are changes in the average number and position of S1 nuclease-sensitive base pair mismatch sites on the majority of the hairpin stems. Our data indicate that during early embryogenesis there are sequence changes in vivo within the majority of the adjacent inverted repeat sequences of the sea urchin genome. We have also found that there is higher specificity for the occurrence of sequence-change events within that fraction of the inverted repeat sequences that are methylated in vivo.

Animals↗
PubMed1995

Consensus inverted terminal repeat sequence of Paramecium IESs: resemblance to termini of Tc1-related and Euplotes Tec transposons.

During the formation of a transcriptionally active macronucleus, ciliated protozoa excise large numbers of interstitial segments of DNA (internal eliminated sequences; IESs) from their chromosomes. In this study we analyze the published sequences of 20 IESs that interrupt surface protein genes of Paramecium and identify a consensus inverted terminal repeat. This sequence is similar to the ends of the Tc1-related transposons found in nematodes and other metazoans, as well as to both the ends of the Tec transposons and at least some of the IESs in the distantly related ciliate Euplotes crassus. The results of these analyses bolster previous proposals that IESs were created by transposition.

Animals↗
PubMed1978

Isolation and characterization of a highly repetitious inverted terminal repeat sequence from Oxytricha macronuclear DNA.

The low-complexity "gene-sized" linear DNA duplexes of the Oxytricha macronucleus sport short inverted terminal repeats; thus, each single strand is capable of forming a circle held together by a duplex "neck" [Wesley, R. D. (1975) Porc. Natl. Acad. Sci. USA 72, 678--682]. We have isolated necks from total, circularized, single-stranded macronuclear DNA by treatment with nuclease S1. Necks represent at least 2.2% of the total DNA, are homogeneous in size (23 base pairs), melt at 55 degrees in 0.18 M Na+, and reassociate extremely rapidly at 22 degrees (Cot1/2 = 1.1 X 10(-5) mol-liter-1.sec) to form hybrid necks of the same thermal stability. From these and other results, we conclude that all necks on all the many thousands of different single-stranded circles are the same. The neck sequence is therefore highly repetitious--found in multiple copies (as inverted terminal repeats at flush duplex ends and probably also internally) on each natural "gene-sized" macronuclear DNA molecule--implying the possible participation of this sequence both in the general vegetative metabolism of macronuclear DNA and in the pre-vegetative process whereby macronuclear DNA is excised from the total Oxytricha genome.

Animals↗
PubMed1981

Rearrangements in the chloroplast genomes of mung bean and pea.

We have mapped all the cleavage sites for the restriction endonucleases BstEII, Kpn I, Pst I, Pvu II, Sac I, Sal I, Sma I, and Xho I on the circular chloroplast chromosomes from mung bean and pea. The mung bean chloroplast genome measures 150 kilobase pairs (kb) in length; it includes two identical sequences of 23 kb that contain the ribosomal genes and are arranged as an inverted repeat separated by single-copy regions of 21 and 83 kb. The pea chloroplast genome is only 120 kb in size, has only one set of ribosomal genes, and does not possess any detectable repeated sequences. The mung bean inverted repeat structure is common to all other nonleguminous higher plant chloroplast genomes studied, whereas the pea structure has been found only in the closely related legume Vicia faba. We conclude from these data that loss of one copy of the inverted repeat sequence has occurred only rarely during the evolution of the Angiosperms, and in the case of the legumes after the divergence of the mung bean line from the pea-Vicia line. We present hybridization data indicating that rearrangements that change the linear order of homologous sequences within the chloroplast genome have been quite frequent during the course of legume evolution.

Journal Article↗
PubMed1990

Mutational analysis of the inverted repeats of Tn3.

The transposase protein and the terminal inverted repeat sequences of the prokaryotic transposon Tn3 are essential for transposition. In order to determine the sequences within the inverted repeat necessary for transposition and interaction with transposase, we have constructed a series of mini-Tn3s in which specific mutations have been introduced into the inverted repeats. The effects of these mutations on transposition have been assayed in vivo using a mating-out transposition assay. Several single base-pair mutations within the transposase binding site reduce transposition frequency. Mutations that affect transposition show a greater effect when present in both inverted repeats than when present in only one inverted repeat.

Base Sequence↗
PubMed1989

Repair of imidazole ring-opened purines in DNA: overproduction of the formamidopyrimidine-DNA glycosylase of Escherichia coli using plasmids containing the fpg+ gene.

The formamidopyrimidine-DNA glycosylase (Fapy-DNA glycosylase) of Escherichia coli (E. coli) was overexpressed by cloning the fpg+ gene on a multicopy plasmid and placing this gene under the control of the lac promoter. The lac promoter contributed significantly to the overall expression of the fpg gene only after the deletion of an inverted repeat sequence located immediately upstream from the fpg promoter. The biological purpose of the inverted repeat sequence may be associated with the termination of an adjacent gene transcribed in the same direction as the fpg gene in E. coli. Cells harboring the fpg gene under the control of the lac promoter were able to produce the Fapy-DNA glycosylase as at least 17% of the total soluble proteins. Such strains allow the preparation of milligram quantities of pure protein for use in the study of its catalytic properties and three dimensional crystal structure.

DNA Damage↗
PubMed1995

Isolation and characterization of Bacillus subtilis groE regulatory mutants: evidence for orf39 in the dnaK operon as a repressor gene in regulating the expression of both groE and dnaK.

An inverted repeat sequence known as CIRCE (controlling inverted repeat of chaperone expression) in the Bacillus subtilis groE operon has been suggested to function as an operator. To identify the regulatory gene directly or indirectly involved in CIRCE-mediated heat-inducible groE expression, B. subtilis WBG2, carrying an integrated groE-bgaB transcription fusion in the amyE locus, was mutagenized. Dark blue colonies formed at 37 degrees C represent mutants which constitutively produce BgaB (a thermostable beta-galactosidase) at high levels. Seven mutants (WBG101 to WBG107) were selected for further characterization. They all overproduced BgaB, GroEL, and DnaK simultaneously at 37 degrees C. These mutants could be restored to normal by introducing a plasmid carrying a functional copy of orf39, the first gene in the B. subtilis dnaK operon. Genomic sequencing of these mutants demonstrated that they all carried a single mutation in orf39. These mutations can be divided into three groups: (i) Gly-307 to Asp, (ii) Ser-122 to Phe, and (iii) Gly-63 to Glu. By using a binary vector system in E. coli, production of ORF39 was found to negatively regulate the expression of groE-bgaB in a CIRCE-specific manner. Under the heat shock condition, the negative regulation mediated by ORF39 was abolished. Mobility shift of the CIRCE-containing probe was also observed with the crude extract prepared from the E. coli strain that overproduced ORF39. Therefore, ORF39 is the negative regulatory factor which regulates both groE and dnaK expression in B. subtilis. It is likely to function as a CIRCE-specific repressor.

Amino Acid Sequence↗
PubMed2004

Inverted terminal repeat sequences of adeno-associated virus enhance the antibody and CD8(+) responses to a HIV-1 p55Gag/LAMP DNA vaccine chimera.

The immune responses to an HIV-1 p55Gag vaccine encoded as a DNA chimera with the lysosomal associated membrane protein-1 (LAMP) have been examined for the effect of the addition of the inverted terminal repeat (ITR) sequences of the adeno-associated virus (AAV) to the DNA plasmid construct, and of packaging the LAMP/gag gene as a recombinant AAV vector (rAAV). DNA plasmids encoding Gag and the LAMP/Gag protein chimera were constructed in two vectors, the pcDNA3.1 and a corresponding plasmid containing the ITR sequences (pITR) flanking the expression elements of the plasmid, and the pITR LAMP/gag DNA plasmid was encapsidated in the rAAV vector. Human 293 cells transfected in vitro with LAMP/gag plasmids either in pcDNA3.1 or pITR produced much Gag protein in cell extracts (1.6 and 2.2 ng of Gag/mg of protein, respectively). The immune responses of mice to immunization with these constructs were examined under three protocols: DNA prime/DNA boost, DNA prime/rAAV boost, and a single rAAV immunization. The results demonstrated that under DNA prime/DNA boost protocol, the "naked" DNA vaccines encoding the LAMP/gag chimera, either as pcDNA3.1 or pITR DNA plasmid constructs, elicited strong CD4(+) T cell responses. In contrast, significantly higher levels of CD8(+) and antibody responses were observed with the pITR-DNA constructs. Immunization with the rAAV vector under the DNA prime/rAAV boost protocol resulted in sustained T cell responses and a markedly increased antibody response, predominantly of the IgG(1) isotype resulting from the activation of the Th2 subset of CD4(+) T cells, that was sustained for at least 5 months after immunization.

Animals↗
PubMed1995

Identification of prophage genes expressed in lysogens of the Lactococcus lactis bacteriophage BK5-T.

Bacteriophage BK5-T is a small isometric-headed temperate phage that infects Lactococcus lactis subsp. cremoris. Northern (RNA) analysis of mRNA produced by lysogenic strains containing BK5-T prophage revealed four major BK5-T transcripts that are 0.8, 1.3, 1.8, and 1.8 kb in size and enabled a transcription map of the prophage genome to be prepared. The position and size of each transcript corresponded closely to the position and size of open reading frames predicted from the nucleotide sequence of BK5-T. Analysis of the transcripts suggested that one of them was derived from the gene encoding the BK5-T integrase and another was from the gene encoding the BK5-T homolog of the lambda cI repressor. Computer analysis of the nucleotide sequence upstream of the BK5-T cI homolog predicted the presence of a pair of divergent promoters and three inverted repeat sequences, features characteristic of temperature-phage immunity regions. By analogy with lambda, the three inverted repeat sequences could be binding sites for cI or Cro homologs and the two divergent promoters could initiate transcription through the BK5-T equivalents of cI and cro.

Amino Acid Sequence↗
PubMed1998

Insertional polymorphism in introns 4 and 10 of the maize beta-glucosidase gene glu1.

The major beta-glucosidase isozyme Glu1 is encoded by a highly polymorphic gene (glu1) in maize. The glu1 gene comprises 12 exons and 11 introns. Two of these introns, introns 4 and 10, show insertional polymorphism: those in allele glu1-1 (represented by inbred line OH7B) are longer than those in other inbred genotypes and in two teosintes (Zea mexicana and Zea parviglumis) surveyed. Sequence data revealed that an increase in the length of intron 4 from 150 to 477 bp in OH7B is due to a short (11 bp) tandem duplication and a large insertion sequence of 313 bp plus a 4-bp (5' ATAG 3') direct repeat. The 313-bp insertion sequence (referred to as mzsTn-1) has all the features of a transposon, having a 25-bp well-conserved (3/25 mismatches) inverted repeat sequence at its termini flanked by a 4-bp direct repeat. The increase in length from 1041 to 1302 bp in intron 10 of OH7B is due to a 259-bp insertion sequence (referred to as mzsTn-2) plus a 2-bp (5' TA 3') direct repeat. The mzsTn-2 element also possesses all the hallmarks of a transposon: a 34-bp well-conserved (3/34 mismatches) inverted repeat sequence at its termini flanked by a 2-bp direct repeat. The mzsTn-1 element belongs to a new family of inverted repeat elements, while mzsTn-2 belongs to the Stowaway family of inverted repeat elements. Analysis of PCR products from amplifications off genomic-DNA templates, using primers derived from the inverted repeat termini, and Southern blotting data suggest that both small transposons are members of a multigene family. The occurrence of two different small transposons in introns of the same glu1 allele in inbred OH7B and their absence in other genotypes suggest that they have moved into this glu1 allele recently through mediation of their autonomous counterparts that are active in OH7B or in its ancestry.

Base Sequence↗
PubMed1995

Resistance of Neisseria gonorrhoeae to antimicrobial hydrophobic agents is modulated by the mtrRCDE efflux system.

The mtr (multiple transferable resistance) system of Neisseria gonorrhoeae determines levels of gonococcal resistance to hydrophobic agents (HAs), including detergent-like fatty acids and bile salts that bathe certain mucosal surfaces. The genetic organization of the mtr system was determined and found to consist of the mtrR gene, which encodes a transcriptional regulator (MtrR), and three tandemly linked genes termed mtrCDE. The mtrCDE genes were organized in the same apparent transcriptional unit, upstream and divergent from the mtrR gene. The mtrCDE-encoded proteins of N. gonorrhoeae were analogous to a family of bacterial efflux/transport proteins, notably the MexABOprK proteins of Pseudomonas aeruginosa and the AcrAE and EnvCD proteins of Escherichia coli, that mediate resistance to drugs, dyes, and detergents. Inactivation of the mtrC gene resulted in loss of the MtrC lipoprotein and rendered gonococci hypersusceptible to structurally diverse HAs; this revealed the importance of the mtr system in determining HAR in gonococci. Further support for a role of the mtrCDE gene complex in determining levels of HAR in gonococci was evident when transformants bearing mutations in the mtrR gene were analysed. In this respect, missense and null mutations in the mtrR gene were found to result in increased levels of MtrC and HAR. However, high levels of MtrC and HAR, similar to those observed for clinical isolates, were associated with a single bp deletion in a 13 bp inverted repeat sequence that intervened the divergent mtrR and mtrC genes. We propose that the 13 bp inverted-repeat sequence represents a transcriptional control element that regulates expression of the mtrRCDE gene complex, thereby modulating levels of gonococcal susceptibility to HAs.

Amino Acid Sequence↗