Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Inverted Repeat Sequences”

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 235 records · Page 13Linked to original sources
PubMed1984

Location and analysis of nucleotide sequences at one end of a putative lac transposon in the Escherichia coli chromosome.

A segment of Escherichia coli DNA that contained a discontinuity of homology with Salmonella typhimurium DNA was isolated. The segment, 1,430 base pairs long, was derived from one end of the lac "loop," a region of about 12 kilobase pairs of E. coli DNA, including the lac operon which has no detectable homology with S. typhimurium DNA (K. Lampel and M. Riley, Mol. Gen. Genet. 186:82-86, 1982). The nucleotide sequence of the 1,430-base-pair segment of DNA was determined. The location of the junction of discontinuity of homology within the segment was established by hybridization experiments. Nucleotide sequences at or near the junction were determined to be similar to sequences that are involved in site-specific inversion in S. typhimurium, E. coli, phage P1, and phage Mu. Similar sequences are also present within the terminal inverted repeat sequences of transposon Tn5 and at the V-D-J joining sequences of eucaryotic immunoglobulin genes. Therefore, the lac operon, together with flanking DNA, may have been inserted into the E. coli chromosome at one time via a site-specific recombination event. Rearrangement events of this kind undoubtedly have played a significant role in the evolutionary divergence of chromosomal DNAs.

Base Composition↗
PubMed1986

A nuclear gene of Saccharomyces cerevisiae needed for stable maintenance of plasmids.

We have isolated host mutants of Saccharomyces cerevisiae in which the 2 microns plasmid is poorly maintained. All the mutants tested constituted one complementation group, which was designated map1 (maintenance of plasmid). Minichromosomes carrying a chromosomal replication origin and a centromere were affected in the mutants. Two types of hybrid plasmids generated in vivo and in vitro appeared to compensate for the mutations and had DNA regions containing multiple ARS (autonomously replicating sequence) or a set of 2 microns inverted repeat sequences. These results suggested that poor maintenance of plasmids was due to low levels of replication, probably at the initiation of replication.

Cell Nucleus↗
PubMed2006

Post-transcriptional gene silencing of GBSSI in potato: effects of size and sequence of the inverted repeats.

In the past, silencing of granule-bound starch synthase (GBSSI) in potato was achieved by antisense technology, where it was observed that inclusion of the 3' end of the GBSSI coding region increased silencing efficiency. Since higher silencing efficiencies were desired, GBSSI inverted repeat constructs were designed and tested in potato. First, large inverted repeats comprising the 5' and the 3' half of the GBSSI cDNA were tested. The 5' IR construct gave a significantly higher silencing efficiency than the 3' IR construct. Since it was not known whether the observed difference was due to the sequence or the orientation of the inverted repeat, the GBSSI cDNA was divided into three regions, after which each region was tested in small inverted repeats in two orientations. To this end large numbers of independent transformants were produced for each construct. The results suggested that there was no effect of inverted repeat orientation on silencing efficiency. The percentage of transformants showing strong inhibition varied from 48% for a 3'-derived construct to 87% for a 5' as well as a middle region-derived construct. Similar to the large inverted repeats, the 3' sequences induced the least efficient silencing implying that the observed differences in silencing efficiency are caused by sequence differences. The small inverted repeat constructs with a repeat size of 500-600 bp and a spacer of about 150 bp were more efficient silencing inducers than the large inverted repeat constructs where the size of the repeat was 1.1 or 1.3 kb whilst the size of spacer was 1.3 or 1.1 kb. The results presented here show that size and sequence of the inverted repeat influenced silencing efficiency.

Blotting, Northern↗
PubMed1986

Identification by antibody to a synthetic peptide of a protein specified by a diploid gene located in the terminal repeats of the L component of herpes simplex virus genome.

In the course of studies on the a sequences located at the termini of and at the junction between the L and S components of herpes simplex virus 1 DNA, J. Chou and B. Roizman (J. Virol. 57:629-637, 1986) noted that the a sequence acted as a gamma 1 promoter when fused to the structural sequence of the thymidine kinase gene, the b inverted repeat sequences located in the L component next to the a sequences contained an open reading frame predicted to encode the protein of 358 amino acids with a molecular weight of 37,054, and the transcription of an RNA homologous to the open reading frame initiated within the a sequence. The nucleotide sequence of the open reading frame predicted the presence of the triplet Ala-Thr-Pro repeated 10 times. To verify the existence of the predicted gene, designated gamma 134.5, a synthetic peptide consisting of the triplet Ala-Thr-Pro repeated 10 times was synthesized and used to raise antibodies in rabbits. The results were as follows. The antiserum to the peptide reacted with a 43,500-apparent-molecular-weight protein present in lysates of cells infected with herpes simplex virus 1 but not present in mock-infected or herpes simplex virus 2-infected cells. We genetically engineered a recombinant virus containing a single copy of a truncated gene. Concordant with predictions, the antibody reacted with a faster-migrating protein in cells infected with this recombinant. The gamma 134.5 gene product was soluble, and it accumulated primarily in the cytoplasm late in infection. The overlap of the domain of the gamma 134.5 gene with the a sequence raises the possibility that it acts in trans on the a sequence and is associated with one of the functions currently ascribed to the a sequences.

Amino Acid Sequence↗
PubMed1994

Repeated sequence target sites for maternal DNA-binding proteins in genes activated in early sea urchin development.

This communication concerns a very highly conserved inverted repeat sequence element that serves as a target site for a sea urchin maternal DNA-binding factor. The maternal factor is present in relatively large amounts in unfertilized eggs, but is about 100 x less prevalent per embryo in 24-hr embryo nuclear extract. The inverted repeat target site is found in the regulatory domain of the CyIIIa cytoskeletal actin gene and also in two upstream genes encoding transcription factors that bind to a functionally important cis-regulatory element of the CyIIIa gene. There are about 460 copies of the inverted repeat target site per genome. About 15% of these sites occur in a nested arrangement together with a second inverted repeat that binds another previously characterized maternal transcription factor. This arrangement is the same as that which occurs in the CyIIIa gene, and it may be of regulatory significance with respect to activation of certain genes in oogenesis and early embryogenesis.

Actins↗
PubMed2000

Sequence analysis of the leftward end of simian varicella virus (EcoRI-I fragment) reveals the presence of an 8-bp repeat flanking the unique long segment and an 881-bp open-reading frame that is absent in the varicella zoster virus genome.

Simian varicella virus (SVV) causes varicella (chickenpox) in nonhuman primates, becomes latent in cranial and dorsal root ganglia, and reactivates to produce zoster (shingles). Because the clinical and molecular features of SVV closely resemble those of varicella zoster virus (VZV) infection of humans, SVV infection of primates has served as an experimental model of VZV pathogenesis and latency. The SVV genome has been completely mapped, but attempts to clone the 3600-bp EcoRI fragment located at the leftward end of the virus genome have hitherto been unsuccessful. Herein, we report the cloning and the complete nucleotide sequence of this region. Comparison of the SVV and VZV sequences in this region revealed an 8-bp inverted repeat sequence flanking the unique long segment of the SVV genome; an 879-bp open-reading frame (ORF) A in SVV that is absent in VZV but has 42% amino acid identity to SVV ORF 4 and 49% to VZV ORF 4; a 342-bp ORF B in SVV with 35% amino acid identity to a 387-bp ORF located to the left of ORF 1 on the VZV genome; and a 303-bp ORF in SVV with 27% amino acid identity to VZV ORF 1. No homologue of VZV ORF 2 was detected. Transcripts specific for ORFs A and B were present in SVV-infected cells in culture and in acutely infected monkey ganglia. Overall, there are more than 2000 bp of DNA in the SVV genome that are absent in the VZV genome.

Amino Acid Sequence↗
PubMed1992

Binding of the Bacillus subtilis spoIVCA product to the recombination sites of the element interrupting the sigma K-encoding gene.

The gene encoding sigma K, a transcription factor controlling mother-cell-specific gene expression at a late stage of sporulation, is interrupted by the skin element in Bacillus subtilis. The skin element is excised from the mother cell chromosome by a DNA rearrangement that depends on the spoIVCA gene product. This protein has no other role in sporulation than promoting skin excision and exhibits sequence similarity to a family of bacterial site-specific recombinases. An expression library of B. subtilis DNA in lambda gt11 was screened for the presence of a gene encoding a protein able to bind in vitro to an oligonucleotide matching the inverted repeat sequences present at the ends of the skin element. Several bacteriophages were found to contain the spoIVCA gene. A cell extract containing the SpoIVCA protein protected the inverted repeats and their neighboring sequences from DNase I digestion and methylation. SpoIVCA decreased the electrophoretic mobility of a DNA fragment containing its binding sequence and simultaneously bent the DNA. A single molecule of SpoIVCA bound initially to the repeat sequence followed by binding of a second molecule to create a complex straddling the recombination site.

Bacillus subtilis↗
PubMed1995

Identification in the human genome of mobile elements spread by DNA-mediated transposition.

We have identified in the human genome two families of mobile elements possessing the sequence characteristics of transposons that move directly from DNA to DNA rather than requiring the reverse transcription of an RNA intermediate. One type of element is closely related to the autonomous transposable element, mariner, and comprises a coding region for a transposase protein flanked by short terminal inverted repeat sequences (TIRs) of 31 or 32 bp. Elements of the second type form a family of short interspersed repetitive elements (SINEs) that are composed simply of two 37 bp TIRs surrounding six unique bps. The TIRs of the human mariner family are identical in all but one position to those of the SINE family, suggesting that the inverted-repeat SINEs represent non-autonomous transposable elements dependent on mariner-type transposase for mobility. Evidence for the mobility of both types of element is provided by examples of their integration into other repeat sequences and by the comparison of orthologous sites in cattle and human genomes. This evidence also shows that these elements have been active in DNA-mediated transposition at some point in the mammalian lineage. Therefore, it appears that the process of DNA-mediated transposition has occurred in mammalian cells and that its maximal cis-requirements are contained in the 80 bp consensus sequence of the human inverted-repeat SINE family.

Amino Acid Sequence↗
PubMed1980

Terminal nucleotide sequences of Tn551, a transposon specifying erythromycin resistance in Staphylococcus aureus: homology with Tn3.

The erythromycin resistance determinant of Staphylococcus aureus plasmid pI258 resides on a 5.3 kb transposon, Tn551. We have determined DNA sequences surrounding the junctions between the transposon and the flanking DNA in the wild-type plasmid, in an insertion into a second plasmid, and in two transposon-related deletions. The ends of the transposon consist of an inverted repeat of 40 base pairs flanked by a direct repeat of 5, thus placing the transposon in the same class as Tn3, IS2, Tn501, gamma delta, and bacteriophage Mu. Interestingly, we find that the terminal sequences of the 40 base pairs inverted repeat are very similar to the ends of Tn3, a transposon which one would not have expected to show any relation to Tn551. This result suggests common ancestry for Tn3 and Tn551. The inverted repeat sequence of Tn551 also contains (with one additional inserted base) the internal heptanucleotide sequence which has been found to be common to most of the transposable elements that generate 5-base pair direct repeat sequences.

Base Sequence↗
PubMed1998

C1 inhibitor gene sequence facilitates frameshift mutations.

Mutations disrupting the function or production of C1 inhibitor cause the disease hereditary angioneurotic edema. Patient mutations identified an imperfect inverted repeat sequence that was postulated to play a mechanistic role in the mutations. To test this hypothesis, the inverted repeat was cloned into the chloramphenicol acetyltransferase gene in pBR325 and its mutation rate was studied in four bacterial strains. These strains were selected to assay the effects of recombination and superhelical tension on mutation frequency. Mutations that revert bacteria to chloramphenicol resistance (Cmr) were scored. Both pairs of isogenic strains had reversion frequencies of approximately 10(-8). These rare reversion events in bacteria were most often a frameshift that involved the imperfect inverted repeat with a deletion or a tandem duplication, an event very similar to the human mutations. Increased DNA superhelical tension, which would be expected to enhance cruciform extrusion, did not accentuate mutagenesis. This finding suggests that the imperfect inverted repeat may form a stem-loop structure in the single-stranded DNA created by the duplex DNA melting prior to replication. Models explaining the slippage can be drawn using the lagging strand of the replication fork. In this model, the formation of a stem-loop structure is responsible for bringing the end of the deletion or duplication into close proximity.

Angioedema↗
PubMed1990

Spontaneous deletion formation within the beta-galactosidase gene of Lactobacillus bulgaricus.

To investigate the genetic stability of the dairy organism Lactobacillus bulgaricus, we have analyzed 107 spontaneous mutations of the beta-galactosidase gene of this organism. Ten of these mutations were DNA rearrangements giving rise to different deletions, located predominantly within a small hot spot area. The DNA sequences of the different deletion junctions have been determined. The analysis showed that the deletions can be divided into two classes, depending on the presence of short direct-repeat sequences at the deletion endpoints and on the length of the deleted sequences. Possible mechanisms of these deletion formations and the involvement of inverted-repeat sequences that may enhance slipped DNA mispairing are discussed.

Base Sequence↗
PubMedDate not supplied

The stacked-X DNA Holliday junction and protein recognition.

The crystal structure of the four-stranded DNA Holliday junction has now been determined in the presence and absence of junction binding proteins, with the extended open-X form of the junction seen in all protein complexes, but the more compact stacked-X structure observed in free DNA. The structures of the stacked-X junction were crystallized because of an unexpected sequence dependence on the stability of this structure. Inverted repeat sequences that contain the general motif NCC or ANC favor formation of stacked-X junctions, with the junction cross-over occurring between the first two positions of the trinucleotides. This review focuses on the sequence dependent structure of the stacked-X junction and how it may play a role in structural recognition by a class of dimeric junction resolving enzymes that themselves show no direct sequence recognition.

Base Sequence↗
PubMed1986

Polypeptides encoded by varicella-zoster virus unique short sequences.

The SalI-I and K DNA fragments which lie within the unique short sequences (Us) and contain a portion of the inverted repeat sequences (IRs/TRs) of varicella-zoster virus (VZV) DNA were cloned in an in vitro transcription vector system (pGEM-2). RNA was transcribed from both strands, translated in vitro and analyzed by SDS-PAGE. The results showed that SalI-I and K each codes for three primary translation products. Polypeptides with Mrs of 19,000 (19K), 47K, 93K/90K are encoded by SalI-I and polypeptides of 12K, 19K, and 50K are encoded by SalI-K. These results are consistent with the predicted genetic expression of the VZV SalI-I and SalI-K DNA fragments.

Cloning, Molecular↗
PubMed1991

Equine herpesvirus 1 sequence near the left terminus codes for two open reading frames.

We have previously reported the sequence of the equine herpesvirus one genomic termini that are homologous to the genomic termini of other herpesviruses. In this paper, we present the nucleotide sequence adjacent to the left terminus sequence (map units 0.0087 to 0.0237). This sequence codes for two open reading frames (ORF) which are homologous to ORF2 and ORF3 of the varicella-zoster virus genome and are located at colinear positions. The L region sequence presented here also contains a segment that is involved in the generation of the genome of EHV-1 DI particles through recombination with sequences mapping within the internal portion of the inverted repeat sequences of the short region.

Amino Acid Sequence↗
PubMed1989

Relationship between the pel genes of the pelADE cluster in Erwinia chrysanthemi strain B374.

In this paper, we have used filter hybridization and nucleotide sequencing to analyse the relationship between the three genes of the pelADE cluster in the Erwinia chrysanthemi (Ech) strain B374. This cluster encodes for three of the five pectate lyase proteins that are involved in the maceration and soft-rotting of plant tissue, an important trait in Ech pathogenicity. Southern hybridization revealed homology between each of the three pel genes. A 3560 bp DNA fragment containing the pelE and pelD genes was sequenced. These two genes show extensive homology in the coding regions but only low homology in the 5' and 3' non-coding regions. However both genes exhibit sequences homologous to the Escherichia coli CAP-binding site consensus sequence upstream of the start codon and an inverted repeat sequence which may act as a rho-independent transcriptional terminator after the translational stop. The pel genes of Ech B374 were also compared with the already sequenced pel genes of EC16, another Ech strain.

Amino Acid Sequence↗
PubMed1995

Structure and function of Tn5467, a Tn21-like transposon located on the Thiobacillus ferrooxidans broad-host-range plasmid pTF-FC2.

A 3.5-kb region of plasmid pTF-FC2, which contains a transposon-like element designated Tn5467, has been sequenced, and its biological activity has been investigated. The transposon is bordered by two 38-bp inverted repeat sequences which have sequence identity in 37 of 38 and in 38 of 39 bp to the tnpA distal and tnpA proximal inverted repeats of Tn21, respectively. Within these borders, open reading frames with amino acid similarity to a glutaredoxin-like protein, a MerR regulatory protein, and a multidrug-resistant-membrane transport-like protein were found. The gene for the glutaredoxin-like protein was expressed in Escherichia coli and enabled growth of a glutathione-requiring E. coli trxA gshA mutant on minimal medium and the reduction of methionine sulfoxide to methionine. In addition, there were two regions which, when translated, had homology to 85% of the N-terminal region of the Tn21 resolvase (tnpR) and to 15% of the C terminus of the Tn21 transposase (tnpA). A region containing res-like sites was located immediately upstream of the partial tnpR gene. Neither the partial transposase nor the resolvase genes of Tn5467 were biologically active, but Tn5467 was transposed and resolved when the Tn21 transposase and resolvase were provided in trans. Tn5467 appears to be a defective transposon which belongs to the Tn21 subgroup of the Tn3 family.

Amino Acid Sequence↗
PubMed1982

Nucleotide sequence of the gene for the M(r) 32,000 thylakoid membrane protein from Spinacia oleracea and Nicotiana debneyi predicts a totally conserved primary translation product of M(r) 38,950.

The gene for the so-called M(r) 32,000 rapidly labeled photosystem II thylakoid membrane protein (here designated psbA) of spinach (Spinacia oleracea) chloroplasts is located on the chloroplast DNA in the large single-copy region immediately adjacent to one of the inverted repeat sequences. In this paper we show that the size of the mRNA for this protein is approximately 1.25 kilobases and that the direction of transcription is towards the inverted repeat unit. The nucleotide sequence of the gene and its flanking regions is presented. The only large open reading frame in the sequence codes for a protein of M(r) 38,950. The nucleotide sequence of psbA from Nicotiana debneyi also has been determined, and comparison of the sequences from the two species shows them to be highly conserved (>95% homology) throughout the entire reading frame. Conservation of the amino acid sequence is absolute, there being no changes in a total of 353 residues. This leads us to conclude that the primary translation product of psbA must be a protein of M(r) 38,950. The protein is characterized by the complete absence of lysine residues and is relatively rich in hydrophobic amino acids, which tend to be clustered. Transcription of spinach psbA starts about 86 base pairs before the first ATG codon. Immediately upstream from this point there is a sequence typical of that found in E. coli promoters. An almost identical sequence occurs in the equivalent region of N. debneyi DNA.

Journal Article↗
PubMed2003

Direct repeat sequences are essential for function of the cis-acting locus of transfer (clt) of Streptomyces phaeochromogenes plasmid pJV1.

The functionality of direct and inverted repeat sequences inside the cis acting locus of transfer (clt) of the Streptomyces plasmid pJV1 was determined by testing the effect of different deletions on plasmid transfer. The results show that the single most important element for pJV1 clt function is a series of evenly spaced 9 bp long direct repeats which match the consensus CCGCACA(C/G)(C/G), since their deletion caused a dramatic reduction in plasmid transfer. The presence of these repeats in the absence of any other clt sequences allowed plasmid transfer to occur at a frequency that was at least two orders of magnitude higher than that obtained in the complete absence of clt. A database search revealed regions with a similar organization, and in the same position, in Streptomyces plasmids pSN22 and pSLS, which have transfer proteins homologous to those of pJV1.

Base Sequence↗