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PubMed1984

Absence of direct repeats flanking transposons resulting from intramolecular transposition.

Tn2660 is an ampicillin-resistance-conferring transposon with a high degree of homology for the transposon Tn3. The nucleotide sequences flanking the termini of Tn2660 have been determined on plasmids inferred to have resulted from both inter- and intramolecular transposition of Tn2660. In all cases, transposition of Tn2660, as of Tn3, creates 5-bp flanking direct repeats, except following intramolecular transposition resulting from trans ligation. In this case, in R6K replicons, the nucleotide sequence between the two Tn2660 elements is stably inverted from the normal orientation, and 5-bp direct repeats do not flank each transposon, but instead flank opposite ends of the two transposon copies.

Base Sequence↗

PubMed1993

Sequence analysis of closely related retrotransposon families from fission yeast.

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

Amino Acid Sequence↗

PubMed2000

Further studies on the GS element. A novel mycobacterial insertion sequence (IS1612), inserted into an acetylase gene (mpa) in Mycobacterium avium subsp. silvaticum but not in Mycobacterium avium subsp. paratuberculosis.

We have recently described the GS element, found in Mycobacterium avium subsp. paratuberculosis (MAP), Mycobacterium avium subsp. silvaticum (MAS) and some isolates of Mycobacterium avium subsp. avium serotype 2 (MAAs2), which contains a set of genes of low GC% content, putatively associated with the biosynthesis, modification and transference of fucose to cell wall glycopeptidolipids. Here we describe a further gene of low GC% content (mpa), within the GS element in MAP. mpa is a putative acetyltransferase with homology to genes directly responsible for host specificity and virulence in Salmonella typhimurium and Shigella flexneri. Unlike other GS genes, strong homologues of mpa have not been found in related species, including Mycobacterium tuberculosis (MTB). In MAP, mpa encodes an ORF of 445aa, however, in MAS and MAAs2 mpa contains a single inserted copy of a novel insertion sequence. This element (IS1612) has two sets of inverted repeats at each terminus and encodes two ORFs with good homologies to transposase and helper proteins of IS21 (E. coli) and IS1415 (R. erythropolis). Sequence comparisons between mpa in MAP and MAS indicate the target site for IS1612 is duplicated on insertion to give a direct repeat at each end of the element. Immediately, downstream of the mpa gene in both MAP and MAS are a group of three genes with good homology to the daunorubicin resistance cluster. This cluster has a high GC% content which suggests a 'border' for the GS element. A short motif present at the beginning of this cluster matches with an inverted repeat of this motif at the beginning of the first gene in the GS element. This encapsulates the whole of this group of low GC% genes in MAP and further suggests its cassette-like nature. Homologues of the GS element in MTB show a marked similarity of organisation, suggesting a parallel role for these genes in both pathogens.

Acetylesterase↗

PubMed1988

P element insertions and rearrangements at the singed locus of Drosophila melanogaster.

DNA from the singed gene of Drosophila melanogaster was isolated using an inversion between a previously cloned P element at cytological location 17C and the hypermutable allele singed-weak. Five out of nine singed mutants examined have alterations in their DNA maps in this region. The singed locus is a hotspot for mutation during P-M hybrid dysgenesis, and we have analyzed 22 mutations induced by P-M hybrid dysgenesis. All 22 have a P element inserted within a 700-bp region. The precise positions of 10 P element insertions were determined and they define 4 sites within a 100-bp interval. During P-M hybrid dysgenesis, the singed-weak allele is destabilized, producing two classes of phenotypically altered derivatives at high frequency. In singed-weak, two defective P elements are present in a "head-to-head" or inverse tandem arrangement. Excision of one element results in a more extreme singed bristle phenotype while excision of the other leads to a wild-type bristle phenotype.

Alleles↗

PubMedDate not supplied

Limited host range Ti plasmids: recent origin from wide host range Ti plasmids and involvement of a novel IS element, IS868.

Agrobacterium tumefaciens biotype III octopine strains have been isolated from grapevine tumors worldwide. They comprise limited and wide host range (LHR and WHR) strains that carry related tumor-inducing (Ti) plasmids with two T-regions, TA and TB. The WHR TA-region resembles the biotype I octopine region, whereas the LHR TA-region is a recent deletion derivative of the WHR TA-region, which lacks the iaa genes and part of the ipt gene. Sequencing of the TA-region of the ubiquitous LHR strain AB3 showed that the deleted region is replaced by an insertion sequence (IS) element, IS868, which resembles the IS51 element of Pseudomonas syringae subsp. savastanoi. The Ti plasmid of LHR strain Ag57 carries essentially the same iaa gene deletion as pTiAB3, but lacks IS868. We propose that the LHR Ti plasmids arose by the recent insertion of an IS868 element into the TA-region of a WHR-type Ti plasmid, followed by transposition to a nearby site. The deletion was caused during the second transposition or by later recombination between the two IS868 copies. Biotype III octopine strains also carry an IS51-like sequence close to the TB iaa genes. Our results confirm and extend earlier observations indicating that IS51-like elements in Pseudomonas and Agrobacterium are associated with iaa genes and played a major role in Ti plasmid evolution.

Agrobacterium tumefaciens↗

PubMed1994

The transposon-like structure of IS26-tetracycline, and kanamycin resistance determinant derived from transferable R plasmid of fish pathogen, Pasteurella piscicida.

Tetracycline (pp-tet), and kanamycin (pp-kan) resistance genes were cloned from a transferable R plasmid of fish pathogen Pasteurella piscicida, and complete nucleotide sequences were determined. The pp-tet was a class D Tet determinant constructed with the tetA resistance gene of 1,182 bp encoding a protein with a deduced molecular mass of 41 kDa and the tetR repressor gene of 654 bp encoding a product of 24 kDa. The pp-tet was highly homologous to the tet(D) of plasmid RA1 isolated from Aeromonas hydrophila with two nucleotide differences in the tetR, and of plasmid pIP173 from Salmonella ordonez with two nucleotide differences in the tetA. The pp-kan contained 813 bp encoding a 31 kDa protein of 271 amino acids, and was classified into type aph-Ic. It was identical to the aphA7 in the IAB operon of pBWH77, in which was originally found an isolate of Klebsiella pneumoniae, in its nucleotide sequences and hybrid promoter construction. The genes were connected by an insertion sequence IS26 of 820 bp, and were flanked by repeated copies in direct orientation at the 3' flanking region of the pp-tetA and in inverted orientation at the 3' flanking region of the pp-kan. The genetic elements are organized like a complex transposon by close linkage of the IS26 and the pp-tet and -kan.

Amino Acid Sequence↗

PubMed1997

A fusion promoter created by a new insertion sequence, IS1490, activates transcription of 2,4,5-trichlorophenoxyacetic acid catabolic genes in Burkholderia cepacia AC1100.

Transposition and transcriptional activation by insertion sequences in Burkholderia cepacia AC1100 were investigated. Two closely related new elements, IS1413 and IS1490, were identified and characterized. These elements are not highly related to other insertion sequences identified in AC1100 or other B. cepacia isolates. Based on their structures and the sequences of the inverted terminal repeats and the putative transposase protein, the insertion elements (IS elements) are similar to IST2 of Thiobacillus ferrooxidans and several related elements. All the IS elements that have been identified in this strain are found in multiple copies (10 to 40), and they have high-level promoter activity capable of stimulating transcription from a distance up to 500 bp from a target gene. Strain AC1100 was originally isolated after prolonged selection for the ability to utilize the herbicide 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) as a sole carbon source. Three IS elements are located near the first gene of the 2,4,5-T catabolic pathway, tftA. IS1490 inserted 110 bp upstream of tftA and created a fusion promoter responsible for constitutive transcription of the gene. Our results confirm the hypothesis that IS elements play a central role in transcription of 2,4,5-T genes and likely have stimulated rapid evolution of the metabolic pathway.

2,4,5-Trichlorophenoxyacetic Acid↗

PubMed1995

Isolation and characterization of Pioneer1, a novel Chlamydomonas transposable element.

During the course of this study a novel family of Chlamydomonas mobile elements has been identified in natural isolate strain 224. The first member of this class to be characterized, a 2.8-kb element named Pioneer1, was trapped in an intron of the nitrate reductase structural gene, NIT1. This element has been cloned and completely sequenced and found to be unusual in structure. Pioneer elements are present in a very low-copy number of three per genome in strain 224. The copy number increased by one upon transposition of Pioneer1. Hybridization of Pioneer1 to a variety of Chlamydomonas strains confirmed that this element differed from previously described Chlamydomonas transposons. It also indicated that related elements are present in low-copy number in natural isolate strains 356 and S1D2, but not in the most commonly used laboratory strains 137c and 21 gr. For these reasons, members of the Pioneer family might prove useful as insertional mutagens.

Animals↗

PubMed1986

Nucleotide sequence of an insertion sequence (IS) element identified in the T-DNA region of a spontaneous variant of the Ti-plasmid pTiT37.

We have identified and determined the nucleotide sequence of an IS element (IS136) of Agrobacterium tumefaciens. This is the first IS element isolated and sequenced from a nopaline type Ti-plasmid. Our IS element has 32/30 bp inverted repeats with 6 mismatches, is 1,313 bp long and generates 9 bp direct repeats upon integration. IS136 has 3 main open reading frames (ORF's). Only ORF1 (159 codons) is preceded by sequences that are proposed to serve functional roles in transcriptional and translational initiation. No DNA sequence homology was found between IS136 and IS66, an IS element isolated from an octopine type Ti-plasmid.

Base Sequence↗

PubMed1986

The F plasmid carries an IS3 insertion within finO.

DNA-DNA hybridization studies support the conclusion that coding sequences of the fertility inhibition gene, finO, are present on the F plasmid and map downstream of the transfer region, entirely within 99.19-2.0 F. In addition, the results indicate that the IS3a element at 100/0-1.26 F is inserted within the F finO coding region. This insertion may have inactivated the finO gene on the F plasmid.

Base Sequence↗

PubMedDate not supplied

[The use of molecular biological methods for the individual characterization of Mycobacterium tuberculosis strains].

The expediency of using molecular biological methods for the evaluation of M. tuberculosis clinical strains by individual genetic certification of circulating M. tuberculosis strains has been substantiated. Considerable genetic heterogeneity of M. tuberculosis strains isolated from patients in different regions of the Russian Federation has been established; this heterogeneity is due to the presence of differences in the number of copies (5-26) of element IS6110 in M. tuberculosis cells.

Base Sequence↗

PubMed1997

Circularized Ac/Ds transposons: formation, structure and fate.

The maize Ac/Ds transposable elements are thought to transpose via a cut-and-paste mechanism, but the intermediates formed during transposition are still unknown. In this work we present evidence that circular Ac molecules are formed in plants containing actively transposing elements. In these circles, transposon ends are joined head-to-head. The sequence at the ends' junction is variable, containing small deletions or insertions. Circles containing deleted Ac ends are probably unable to successfully reintegrate. To test the ability of circles with intact transposon ends to integrate into the genome, an artificial Ds circle was constructed by cloning the joined ends of Ac into a plasmid carrying a plant selectable marker. When such a circular Ds was introduced into tobacco protoplasts in the presence of Ac-transposase, no efficient transposase-mediated integration was observed. Although a circular transposition intermediate cannot be ruled out, the findings of circles with deleted transposon ends and the absence of transposase-mediated integration of the circular Ds suggest that some of the joined-ends-carrying elements are not transposition intermediates, but rather abortive excision products. The formation of Ac circles might account for the previously described phenomenon of Ac-loss. The origin of Ac circles and the implications for models of Ac transposition are discussed.

Chromosomes↗

PubMedDate not supplied

E. coli ribosomal RNA contains sequences homologous to insertion sequences IS1 and IS2.

The insertion sequence (IS) elements, IS1 and IS2, present in multiple copies in the Escherichia coli chromosome, are transposable genetic elements of known nucleotide sequence. These elements can modulate gene expression, but it is not known whether they normally function in genetic control. To determine whether IS elements could exert control through specific RNA transcripts, we hybridised lambda NNC1857 r14 (carrying IS1) and pBR322 (carrying a portion of IS2) to Northern blots of E. coli RNA. Regions of homology between the IS elements and ribosomal RNA were observed. Computer analysis of reported nucleotide sequences detected large segments of homology between the IS elements and both 23S and 16S rRNA. Additional homologous sequences in phi X174 and a leader region of a ribosomal protein gene cluster were also detected. The homologous sequence between IS2 and 16S rTNA is the same sequence in phi X174 DNA which codes for the ends of the E and D gene and the start of J. The partial IS sequences may represent silent evolutionary remnants or they could modulate the expression of genes carrying these sequences.

Base Sequence↗

PubMed2006

[A modifier of the Bg element of the Bg-rbg transposable element system of maize].

A modifier of the Bg autonomous element of the Bg-rbg system of transposable elements has been found in the genotype of the inbred maize strain 346. In the presence of this modifier (termed Mbg), the frequency of reversion of mutable allele o2-lf in combination with the Bg-lf element increases by 7-24 times. An increase in the Mbg dosage by three times increases the o2-lf reversion frequency by a factor of about two. The presence of Mbg and Bg-lf in the same genotype before meiosis is necessary for the expression of the Mbg modifying effect. The possible nature and mechanism of action of the novel modifier are discussed.

Alleles↗

PubMed1985

A frameshift mutation at the junction of an IS1 insertion within lacZ restores beta-galactosidase activity via formation of an active lacZ-IS1 fusion protein.

The insertion of IS1 elements into lacZ results in the loss of beta-galactosidase activity, and such insertions exert a severe polar effect on the expression of the distal genes of the operon. In addition to these properties, the mutation lacZ::IS1-MS319 has the unique property of reversion to Lac+ (ts) spontaneously or after treatment with the frameshift mutagen ICR-191; such revertants retain the IS1 element. We have determined that the site of integration of IS1 into lacZ is at position 4338, 18 nucleotides from the end of the sequence encoding the C-terminus of beta-galactosidase. Reversion to Lac+ promoted by ICR-191 results from the loss of a G residue from a GGG sequence located at the junction of lacZ and IS1. As a result an active, but temperature-sensitive, lacZ-IS1 fusion protein is formed containing six amino acids derived from IS1 which replace six amino acids encoded by lacZ. The IS1 element in MS319 is a new member of the iso-IS1 family, which we designate IS1T.

Base Sequence↗

PubMed1992

Recombination between adenovirus type 12 DNA and a hamster preinsertion sequence in a cell-free system. Patch homologies and fractionation of nuclear extracts.

We have previously described a cell-free recombination system derived from hamster cell nuclear extracts in which the in vitro recombination between a hamster preinsertion sequence, the cloned 1768 base-pair p7 fragment, and adenovirus type 12 (Ad12) DNA has been demonstrated. The nuclear extracts have now been subfractionated by gel filtration on a Sephacryl S-300 column. The activity promoting cell-free recombination elutes from the Sephacryl S-300 matrix with the shoulder and not the peak fractions of the absorbancy profile. By using these protein subfractions, in vitro recombinants have been generated between the p7 preinsertion sequence and the 60 to 70 map unit fragment of Ad12 DNA, which has previously shown high recombination frequency. In all of the analyzed recombinants thus produced in vitro, striking patchy homologies have been observed between the p7 and Ad12 junction sequences, and between Ad12 DNA or p7 DNA and pBR322 DNA. The patchy homologies are similar to those found earlier during the analyses of some of the junction sequences in integrated Ad12 genomes in Ad12-induced hamster tumor cell lines. Proteins in the shoulder fractions of the gel-filtration experiment can form specific complexes with double-stranded synthetic oligodeoxyribonucleotides corresponding to several p7 and Ad12 DNA sequences. These sequences participate in the recombination reactions catalyzed by the same column fractions in the shoulder of the absorbancy profile. Such proteins have not been found in the peak fractions. Further work will be required to ascertain that the cell-free recombination system mimics certain elements of the mechanisms of integrative recombination and to purify the cellular components essential for recombination.

Adenoviridae↗

PubMed1991

Identification and DNA sequence of a new Bacteroides fragilis insertion sequence-like element.

A new Bacteroides fragilis insertion sequence (IS)-like element has been identified, cloned, and sequenced. The element is 1598 base pairs in length. It is flanked by a 15-base pair imperfect inverted repeat and contains a large open reading frame which could encode a 430 amino acid protein. There is an 8-base pair duplication of genomic DNA sequences at the site of integration. One copy of the IS-like element is integrated within the 5' upstream sequence of the metallo-beta-lactamase gene ccrA, cloned from B. fragilis TAL3636. The IS-like element is integrated 19 bp upstream of the predicted initiation codon and, therefore, probably provides the transcriptional start signals for the CcrA gene.

Amino Acid Sequence↗

PubMed1990

A wide variety of DNA sequences can functionally replace a yeast TATA element for transcriptional activation.

We created a library of DNA molecules in which the required TATA element of a yeast gal-his3 promoter is replaced by random-sequence oligomers averaging 16 bp in length. Surprisingly, 1% of such random sequences functionally replace the native yeast TATA element. In many cases, sequences completely unrelated to the consensus TATA element (TATAAA) stimulate transcription with equal or increased efficiency. Transcription mediated by these synthetic elements requires GAL4 and is initiated from normal his3 initiation sites, suggesting that it occurs by a mechanism indistinguishable from that involving wild-type TATA elements. Many, but not all, of these elements act as substrates for yeast TFIID in reconstituted transcription reactions in vitro. These observations indicate that yeast TFIID can stimulate transcription from TATA elements whose sequences differ from the consensus, and they suggest the possibility of alternative factors that may provide a related function for transcriptional activation.

Animals↗