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 415 records · Page 23Linked to original sources
PubMed2006

Autonomous cytoplasmic linear plasmid pPac1-1 of Pichia acaciae: molecular structure and expression studies.

The genome organization of the linear DNA-element pPac1-1 from Pichia acaciae was determined. It turned out to be the smallest autonomous cytoplasmic yeast plasmid known so far, consisting of only 12 646 bp, carrying the shortest terminal inverted repeats yet found (138 bp). As for other cytoplasmic linear yeast plasmids, it is characterized by a strikingly high A + T content (75.35%). Ten putative genes (open reading frames, ORFs) reside on the element, leaving only 2.9% of the sequence outside a coding region. Highest similarities of the predicted proteins were obtained for proteins encoded by the three hitherto known autonomous cytoplasmic linear yeast plasmids. Amino acid sequences correspond to predicted polypeptides encoded by ORFs 2-11 of the linear plasmids pGKL2 of Kluyveromyces lactis, pSKL of Saccharomyces kluyveri and pPE1B of Pichia etchellsii. As for the latter, ORF1 existing on the two other plasmids is lacking on pPac1-1. Consistent with cytoplasmic localization, a cytoplasmic promoter termed upstream conserved sequence (UCS) is located in front of each reading frame. RT-PCR transcript analyses for ORFs 8, 9 and 11 proved expression of such genes but functions could not be attributed. The genome organization of pPac1-1 and other autonomous linear elements was found to be almost congruent, irrespective of the accompanying smaller elements, which may or may not encode their own element-specific DNA polymerases.

Amino Acid Sequence↗
PubMed1994

Genes of the linear mitochondrial DNA of Williopsis mrakii: coding sequences for a maturase-like protein, a ribosomal protein VAR1 homologue, cytochrome oxidase subunit 2 and methionyl tRNA.

The mitochondrial DNA (mtDNA) in some yeasts has a linear structure with inverted terminal repeats closed by a single-stranded loop. These mtDNAs have generally a constant gene order, beginning with a small ribosomal RNA gene at the right end and terminating with a cytochrome oxidase subunit 2 gene (COX2) at the left end, independently of the wide variation in genome size. In the mtDNAs from several species of the genus Williopsis, we found an additional open reading frame, ORF1, which was homologous to the Saccharomyces cerevisiae RF1 gene encoding a group I intron maturase-like protein. ORF1 genes from W. mrakii and W. suaveolens were mapped and sequenced. Next to ORF1, COX2 and methionyl tRNA genes were present on the opposite strand. The same relative positions of genes in the mtDNAs so far examined suggests that the constancy of gene order is generally conserved also at the level of individual tRNA genes. We identified another open reading frame, ORF2, in W. mrakii mtDNA. It was mapped next to the cytochrome oxidase subunit 3 gene. Rich in adenine-thymine bases, ORF2 appears to be a homologue of the VAR1 gene which codes for a small ribosomal subunit protein in S. cerevisiae mitochondria. Nucleotide sequences data have been deposited in the EmBL data library under the following Accession Numbers: X66594 (Apocytochrome b and ORF2 genes of W. mrakii), X66595 (ORF1, tRNA-Met and COX2 genes of W. mrakii), X73415 (tRNA-Met and COX2 genes of W. suaveolens), X73416 (ORF1 gene of W. suaveolens) and X73414 (tRNA-Met and COX2 genes of P. jadinii).

Amino Acid Sequence↗
PubMed2001

A Rep recognition sequence is necessary but not sufficient for nicking of DNA by adeno-associated virus type-2 Rep proteins.

The strand-specific, site-specific endonuclease (nicking) activity of the Rep68 and Rep78 (Rep68/78) proteins of adeno-associated virus type 2 (AAV) is involved in AAV replication, and appears to be involved in AAV site-specific integration. Rep68/78 cuts within the inverted terminal repeats (ITRs) of the AAV genome and in the AAV preferred integration locus on human chromosome 19 (AAVS1). The known endonuclease cut sites are 11-16 bases away from the primary binding sites, known as Rep recognition sequences (RRSs). A linear, double-stranded segment of DNA, containing an RRS and a cut site, has previously been shown to function as a substrate for the Rep68/78 endonuclease activity. We show here that mutation of the Rep recognition sequence, within such a DNA segment derived from the AAV ITRs, eliminates the ability of this substrate to be cleaved detectably by Rep78. Rep78 nicks the RRS-containing site from AAVS1 about half as well as the linear ITR sequence. Eighteen other RRS-containing sequences found in the human genome, but outside AAVS1, are not cleaved by Rep78. These results may help to explain the specificity of AAV integration.

Animals↗
PubMed1996

Identification of mutant adeno-associated virus Rep proteins which are dominant-negative for DNA helicase activity.

Adeno-associated virus type 2 (AAV) Rep proteins have been postulated to play a role in unwinding the 145-bp inverted terminal repeats during AAV DNA replication. Previous studies showed that AAV Rep78 and Rep68 could unwind a DNA partial duplex of 26 bp. In this work it is demonstrated that nuclear extracts of human 293 cells containing wild-type Rep68 can unwind partial DNA duplexes up to 160 bp long. Mutant Rep proteins with either a histidine substituted for lysine 340 or a deletion of methionine 225 had no detectable helicase activity and inhibited the helicase activity of wild-type Rep68 protein. This observation is consistent with the model that the functional form of the Rep proteins is a multimer.

Adenosine Triphosphate↗
PubMed1999

Folyt1, a new member of the hAT family, is active in the genome of the plant pathogen Fusarium oxysporum.

An active transposable element, Folyt1, has been isolated from the tomato pathogen Fusarium oxysporum f. sp. lycopersici as an insertion sequence within the coding region of the nitrate reductase gene (nit 1) in two independent mutants (CO66 and CO108). Folyt1 was 2615 bp in length and contained 9-bp imperfect inverted terminal repeats (ITRs) and 8 bp duplicated at the target site upon insertion. The element contained a long open reading frame interrupted by a single putative intron. The predicted amino acid sequence showed similarity to conserved domains of transposases from hobo, Ac, and Tam3 elements, which belong to the hAT family. The excision frequency of Folyt1 was determined to be less than 10(-5) in both mutants. These events restored the nit 1 wild-type allele without leaving footprints in all the revertants of strain CO66. Nevertheless, some revertants of strain CO108 showed a point mutation footprint at the target sequence. Expression of the Folyt1 transposase was detected by Northern analysis as a 2.1-kb transcript. The element exists in about 10 copies per genome in F. oxysporum f. sp. lycopersici and appears to be widely distributed among different formae speciales of F. oxysporum.

Amino Acid Sequence↗
PubMed1994

Genetic evidence for IS1 transposition regulated by InsA and the delta InsA-B'-InsB species, which is generated by translation from two alternative internal initiation sites and frameshifting.

Insertion sequence IS1 contains two reading frames, insA and B'-insB, which are responsible for its transposition, and was previously shown to express two proteins. The first, InsA, is the product of insA. The second, InsA-B'-InsB is a fusion of InsA with the product of B'-insB. Synthesis of this protein occurs by a -1 frameshift from the 3' region of the insA frame to the open reading frame B', extending from the 5' end of the insB frame. Here, I have shown genetically that IS1 encodes the third species delta InsA-B'-InsB: delta InsA-B'-InsB uses two alternative initiation codons in the middle of the insA frame, and is produced by a frameshift mechanism similar to that used in InsA-B'-InsB expression. Deletion of the small region preceding these initiation codons resulted in decreased expression of delta InsA-B'-InsB, suggesting that the small region play some role in the translation initiation. Surprisingly, it was found that delta InsA-B'-InsB has a transposase-like function and InsA can stimulate the transposition promoted by delta InsA-B'-InsB, while delta InsA-B'-InsB seemed to bind to the left terminal inverted repeat (IRL) of IS1 and inhibit transposition when it was present in excess, as well as InsA represses transposition. It is likely that IS1 transposition activity depends on the ratio of InsA to delta InsA-B'-InsB. A double missense mutation of the internal initiation codons resulted in decreased cointegration activity, showing that delta InsA-B'-InsB is responsible for transposition but InsA-B'-InsB is probably not. Some IS elements, which also contain two tandem, out-of-phase, overlapping genes, appear to express deleted fusion proteins like delta InsA-B'-InsB, but the functions are unknown. The complex phenomena of transposition and its control found in IS1 may be more general in the other mobile DNAs.

Amino Acid Sequence↗
PubMed1995

Rescue and replication signals of the adeno-associated virus 2 genome.

The adeno-associated virus 2 (AAV) genome is a single-stranded DNA which contains the inverted terminal repeats (ITRs) of 145 nucleotides. The terminal 125 nucleotides of each ITR form palindromic hairpin structures that serve as primers for AAV DNA replication. These hairpin structures also play a crucial role in the integration, as well as the rescue, of the proviral genome from latently-infected cells, or from the recombinant AAV plasmids. However, the ITRs also contain an additional domain, designated the D-sequence, a 20-nucleotide stretch that is not involved in the formation of hairpins. In order to examine the role of the D-sequence in viral DNA rescue and replication, a number of recombinant AAV plasmids were constructed which contained deletions/substitutions in different regions of the ITRs. The results presented here reveal the existence of additional sequences, other than the hairpin structures, which serve as primers for AAV DNA replication. The results also show that whereas the hairpin structures are sufficient for excision and replication of the viral DNA, the D-sequence is crucial for the high efficiency of rescue and replication of the AAV genome.

Base Sequence↗
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↗
PubMed2002

Generation of helper-dependent adenoviral vectors by homologous recombination.

Helper-dependent adenoviral vectors (HD-Ad) represent a potentially valuable tool for safe and prolonged gene expression in vivo. The current approach for generating these vectors is based on ligation of the expression cassette into large plasmids containing the viral inverted terminal repeats flanking "stuffer" DNA to maintain a final size above the lower limit for efficient packaging into the adenovirus capsid (approximately 28 kb). The ligation to produce the viral plasmid is generally very inefficient. Similar problems in producing first-generation adenoviral (FG-Ad) vectors were circumvented with the development of a system taking advantage of efficient homologous recombination between a shuttle plasmid containing the expression cassette and a FG-Ad vector backbone in the Escherichia coli strain BJ5183. Here we describe a method for fast and efficient generation of HD-Ad vector plasmids that can accommodate expression cassettes of any size up to 35 kb. To validate the system, we generated a HD-Ad vector expressing the fusion protein between beta-galactosidase and neomycin resistance genes under the control of the SR alpha promoter, and one expressing the enhanced green fluorescent protein under the control of the cytomegalovirus promoter. The viruses were rescued and tested in vitro and for in vivo expression in mice. The data collected indicate the possibility for achieving a high level of hepatocyte transduction using HD-Ad vectors derived from plasmids obtained by homologous recombination in E. coli, with no significant alteration of liver enzymes and a less severe, transient thrombocytopenia in comparison with previous reports with similar doses of a FG-Ad vector.

Adenoviridae↗
PubMed1993

pClK1 and pClT5--two linear mitochondrial plasmids from unrelated Claviceps purpurea strains: a comparison.

pClT5, a linear mitochondrial (mt) plasmid from Claviceps purpurea, strain T5, was sequenced and compared to pClK1, a linear mt plasmid from an unrelated C. purpurea strain. Both plasmids have terminal proteins (TPs) at their inverted terminal repeats (TlR). The TlRs of both plasmids show short conserved sequences, which are probably involved in plasmid transcription and replication. The coding capacity of pClT5 and pClK1 is similar: there are two large ORFs (ORF1 and ORF2) homologous to the DNA and RNA polymerase ORFs of pClK1 and several small hydrophobic ORFs. ORF3 shows homology to a small ORF of the Neurospora crassa mt plasmid maranhar and is transcribed. ORF6 of pClT5 is homologous to ORF4 of pClK1; both are transcribed and are possible candidates for the TP encoding ORF.

Base Sequence↗
PubMed1994

Characteristics of IS401, a new member of the IS3 family implicated in plasmid rearrangements in Pseudomonas cepacia.

We have determined the nucleotide sequence of IS401, an insertion sequence implicated in rearrangements of a 170-kb cryptic plasmid from Pseudomonas cepacia. Our analysis focused on a 4066-bp plasmid fragment containing adjacent copies of IS401 and of IS408, an element reported previously to activate gene expression in P. cepacia. One objective was to determine if an apparent increase in the copy number of IS401 in strains carrying adjacent plasmid copies of these two elements might be due to readthrough transcription of an IS401 transposase gene from an outwardly directed promoter within IS408. This possibility was ruled out by nucleotide sequence analysis of the 4066-bp plasmid fragment, which indicated that the major open reading frames of IS401 were oriented in the direction of IS408. IS401 was 1316 bp in length and had 26-bp terminal inverted repeats flanked by 3-bp direct duplications of adjacent DNA. It was closely related to the IS3 family elements IS51 from P. savastanoi and IS3411 from Escherichia coli. Pertinent features of IS408 are also discussed.

Amino Acid Sequence↗
PubMed1994

Nucleotide sequence of the Pseudomonas aeruginosa insertion sequence IS222: another member of the IS3 family.

Sequence analysis of the Pseudomonas aeruginosa insertion sequence element IS222 revealed it to be 1234 bp in size with 23 bp imperfect terminal inverted repeats. Insertion caused a 5-bp duplication of the insertion site. Two ORFs were identified, one of which, ORFA, could encode a basic (pI 10.5) polypeptide with a mass of 11,709. This sequence bears strong homology to the putative ORFA product from the Shigella dysenteriae insertion sequence element IS911, which is a member of the IS3 family of insertion elements. As with other members of this group the nucleotide sequence contains a "frameshift window" (AAAAAAG; M. Chandler and O. Fayet (1993). Mol. Microbiol. 7, 497-503) at which ribosome slippage can result in a fusion protein (ORFAB).

Amino Acid Sequence↗
PubMed1994

IS1032 from Acetobacter xylinum, a new mobile insertion sequence.

IS1031 elements constitute a family of related insertion sequences (IS) in Acetobacter xylinum strains. A new IS1031-related element, IS1032, was isolated from A. xylinum ATCC 23770. Southern hybridization analysis showed that one or more sequences similar to IS1032 are present in most of the A. xylinum strains examined. In addition, one copy was detected in Acetobacter aceti ATCC 15973. The transposition of IS1032 was evident from the appearance of an extra insertion in a spontaneous exopolysaccharide-negative mutant of A. xylinum ATCC 23770. IS1032 consists of 916 bp and has imperfect terminal inverted repeats of 14 bp (IR-Left) and 16 bp (IR-Right). A 3-bp target sequence is duplicated upon insertion. IS1032 displays a single open reading frame, encoding a putative 276-amino-acid protein sharing 58% identity with the corresponding protein encoded by IS1031. Thus, IS1032 is a member of the IS1031 family in A. xylinum. A striking degree of nucleotide sequence similarity between IS1032 and ISRm4 from Rhizobium meliloti was found. Furthermore, the IS1031-family transposases also display stretches of amino acid sequence similarities with putative transposases encoded by IS elements from other species.

Amino Acid Sequence↗
PubMed1995

Characterization of IS1167, a new insertion sequence in Streptococcus pneumoniae.

A new insertion sequence in Streptococcus pneumoniae was identified as a 1435-bp segment of the genome containing 24-bp terminal inverted repeats and flanked by 8-bp direct repeats. A copy of the element, named IS1167, adjacent to the comAB genes was sequenced; seven additional copies were found in the genome of strain CP1200 and relatives descended from strain R36A. Among 22 independent pneumococcal isolates, 11 contained copies of elements hybridizing to IS1167 in nine distinct restriction fragment patterns, with 3-12 copies each. The bulk of the element was occupied by two overlapping open reading frames, encoding basic proteins which together exhibited strong similarity to the full length of the putative transposase of the staphylococcal transposable element, IS1181, as well as significant similarity to those of seven additional known or putative insertion sequences related to the mycobacterial element, IS1096.

Amino Acid Sequence↗
PubMed1997

Cloning and characterization of a high-copy-number novel insertion sequence from chemolithotrophic Thiobacillus ferrooxidans.

Two distinct families of repetitive DNA elements (1.4 and 1.2 kb) were identified from S1 nuclease-treated genomic DNA of four strains of Thiobacillus ferrooxidans. The 1.4-kb fragment hybridized with IST2, an insertion sequence of T. ferrooxidans. The 1.2-kb fragment was cloned and sequenced. The sequence (IST445), 1219 bp in length, with features characteristic of an insertion element, has a terminal inverted repeat of 8 bp, which can be further extended to 23 or 48 bp with 9 and 26 mismatches, respectively. It displays 54.4% identity in 967 nucleotides of overlap with ISAE1 of Alcaligenes eutrophus. The IST445 contains three open reading frames which have codon usage almost similar to 56 different coding genes of T. ferrooxidans. In Southern blots of restricted genomic DNAs probed with IST445, each of the several strains of T. ferrooxidans gives a distinctive fingerprint. IST445 is present in the range of 10-20 copies per genome in the four strains studied.

Amino Acid Sequence↗
PubMed1998

Characterization of a novel insertion sequence, IS1194, in Streptococcus thermophilus.

A novel insertion sequence, IS1194, has been identified in the lactic acid bacterium Streptococcus thermophilus CNRZ368. This 1200-bp element has 16-bp imperfect terminal inverted repeats. The single large open reading frame of this element encodes a 332-amino-acid protein that displays similarities with transposases encoded by bacterial insertion sequences belonging to the IS5 group of the IS4 family. A single copy of IS1194 was detected by hybridization in only 2 of the 19 S. thermophilus strains tested and in 4 of the 13 Lactococcus lactis strains investigated. This suggests that this IS element was acquired by horizontal transfer. The unique IS1194 copy of S. thermophilus CNRZ368 is located in a region of at least 12 kb that was probably acquired by horizontal transfer from L. lactis. Furthermore, the IS1194 right end is identical to sequences found in a broad-host-range conjugative plasmid from Streptococcus pyogenes, pSM19035.

Amino Acid Sequence↗
PubMed1998

Isolation and characterization of IS1416 from Pseudomonas glumae, a new member of the IS3 family.

Isolation and characterization of four different insertion sequence (IS) elements from Pseudomonas glumae MAFF 302744 through transposition into the entrapment vector pSHI1063 are described. One of the elements, IS1416, was further characterized. IS1416 is 1322 bp long and carries 29-bp terminal inverted repeats flanked by a 3-bp direct duplication. IS1416 contains three open reading frames (ORFs), which are designated ORFA1, ORFA2, and ORFB, on one strand. Both DNA sequence of IS1416 and the deduced amino acid sequences of its ORFs strongly suggest that IS1416 is a member of the IS3 family, and is closely related to IS401 from Pseudomonas cepacia and IS51 from Pseudomonas syringae. To our knowledge, IS1416 is the first IS element isolated from P. glumae. The gene organization and possible regulation of transposition functions of IS1416 are also discussed.

Amino Acid Sequence↗
PubMed1999

The first detection of the insertion sequence ISW1 in the intracellular reproductive parasite Wolbachia.

Wolbachia are maternally inherited intracellular rickettsia-like bacteria known to infect a wide range of arthropods. They are associated with a number of different reproductive phenotypes in their hosts, such as cytoplasmic incompatibility, parthenogenesis, and feminization. We report on a novel insertion sequence (IS), ISW1, which was identified in the region downstream of groEL of a Wolbachia strain, wTai. The 573-bp-long ISW1 sequence is the first IS element observed in this organism, displays significant similarity to IS200, and lacks terminal inverted repeats. There were more than 20 copies of ISW1 on the chromosome of wTai. Sequence analysis of nine distinct ISW1 copies and their flanking regions showed that the copies were identical and suggested that ISW1 has no preference for its insertion sites. Possible roles of ISW1 in the adaptation of Wolbachia to intracellular environments and in various reproductive alterations caused by this bacterium are discussed.

Amino Acid Sequence↗