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[Physical mapping of Streptomyces coelicolor A3(2) actinophages. VII. Formation of deletions in the region of phi C43 insertion sequence].

The correlation between the plaque morphology and the presence of the insertion sequence at the phage genomes have been found for different variants of phi C43, obtained by spontaneous induction of strain S. lividans 803. Phages carrying complete insertion have Tum phenotype and they are represented in 4% of induced lysate. Phages carrying the part of insertion have Tu phenotype, their portion in induced lysate is about 26%. Phages without insertion have Stu phenotype and they are the majority of the lysate (70%). All variants phi C43, except wild-type phage, have lost the fragment of phage genome. Phage phi C43ins1, carrying the complete insertion give rise spontaneously at the frequency 10(-2) to deletion derivatives. Heteroduplex experiments show that in the deletion derivatives phi C43ins1 also in the Stu and Tu variants phi C43 one of the termini of the deletions is located within the insertion or at its end. Considerable portion of deletion variants in induced lysate phi C43 also the formation of deletion derivatives phi C43ins1 with high frequency strongly suggest that insertion sequence generates deletions similar to IS of Tn elements.

Bacteriophages↗
PubMed1981

The nucleotide sequence and protein-coding capability of the transposable element IS5.

The nucleotide sequence of IS5, a bacterial insertion sequence, has been determined. It is 1195 bp long and contains an inverted terminal repetition of 16 bp with one mismatch. One open reading frame, spanning nearly the entire length of the element, could encode a polypeptide of 338 amino acids. Upon insertion into a DNA segment, IS5 causes a duplication of 4 bp. Based on seven examples, this site of insertion appears to be nonrandom, and the consensus target site sequence is C . T/A . A . G/A (or C/T . T . A/T . G on the opposite strand). The nucleotide sequences of IS5 insertions into the B and cim genes of bacteriophage Mu have allowed tentative identification of the protein-coding frames of B and cim.

Bacteriophage mu↗
PubMed1985

Molecular interactions between the components of the En-I transposable element system of Zea mays.

The sequence of the Inhibitor element Spm-I8 isolated from the wx-m8 allele has been determined. The element is 2242 bp in length. Its ends can be folded into long stem and loop structures. In a line containing the autonomous En element (wx-m8+En) we have detected a 2.5-kb transcript hybridizing to Spm-I8. A cDNA copy of this En-specific transcript containing 1.2 kb of the 3' end was cloned and it DNA sequence was determined. The 3' half of the cDNA is homologous to Spm-I8 and the region of homology is interrupted by intervening sequences. In the absence of an autonomous En element two chimeric transcripts are observed in the wx-m8 line which are probably initiated at the wx promoter and terminate in the Spm-I8 insertion. In the presence of the En element, these transcripts are suppressed, possibly by a trans-acting function of En, inhibiting transcription read-through into Spm-I8.

Alleles↗
PubMed2001

Position effect of the excision frequency of the Antirrhinum transposon Tam3: implications for the degree of position-dependent methylation in the ends of the element.

We identified eight independent Tam3 copies residing in the same Antirrhinum majus genome. All the copies showed excision at 15 degrees C, but not at 25 degrees C. Under conditions promoting excision, each copy appeared to transpose in the leaves and flower lobes with a nearly constant frequency, whereas individual transposition abilities varied widely: the most active copy had an excision frequency more than 100-fold greater than that of the least active one. Despite the different transposition abilities, the structures of the eight Tam3 copies were almost identical. These results made it clear that the transpositional ability of Tam3 is regulated by chromosomal position, but they do not imply position-dependent transposase activity. The position effect of the Tam3 transposition was found to be correlated to the methylation state of the copy's end regions: DNA methylation in the Tam3 end regions tended to suppress the excision activity, and the degree of methylation was dependent on the chromosomal position. Our results also provide evidence of de novo methylation provoked by transposition of the endogenous element. We propose a mechanism of transpositional regulation of plant transposons that responds to the degree of methylation as determined by chromosomal position.

Blotting, Southern↗
PubMed1985

Tn5 transposes independently of cointegrate resolution. Evidence for an alternative model for transposition.

The replicon fusion model for transposition predicts that each transposable element encodes a site-specific recombination activity (resolvase). A series of experiments were performed to test for the presence of such a resolvase in Tn5. None could be found when assays were devised to detect inter- or intramolecular recombination. An experiment was performed to determine if expression of resolvase occurs simultaneously with the transposition process, thus explaining the undetectable levels of site-specific recombination. In this case, no resolvase activity could be detected in cells that had undergone transposition. Instead, rearrangements were found that could be explained best by an alternative model of transposition. The rearrangements were consistent with a pathway that invokes excising the transposon from its initial site of insertion, followed by circularization of the element before its eventual transposition. The excision event may occur either with or without DNA synthesis.

Ampicillin↗
PubMed1995

Assay for movement of Lepidopteran transposon IFP2 in insect cells using a baculovirus genome as a target DNA.

Mutagenesis of baculoviruses by host mobile elements occurs spontaneously and frequently during propagation of the viruses in Lepidopteran cell cultures. Most of the transposons identified as insertions in baculovirus genomes are relatively small Class II elements that exhibit a remarkable specificity for TTAA target sites. We have developed a transposition assay to analyze the movement of these TTAA-specific Lepidopteran transposons using the baculovirus genome as a target and a lacZ gene under control of the polyhedrin gene promoter as a selective marker for the transposon. This assay provides the first demonstration that a Lepidopteran transposon is capable of transposing while carrying a marker gene in insect cells. The data generated from this assay provide strong evidence that IFP2 encodes a protein that facilitates its own movement. This element may be used in a manner analogous to the P-element to mobilize genes in at least some Lepidopteran insect cells. Transposon tagging within the baculovirus genome identified several known genes and two previously undescribed open reading frames as nonessential to in vitro replication of the virus.

Animals↗
PubMed1993

Sequence and characterization of an insertion sequence, IS711, from Brucella ovis.

The nucleotide (nt) sequence of a previously discovered insertion in Brucella ovis was determined and found to have the hallmarks of an insertion sequence (IS). The element, designated IS711, of 842 bp, is similar in G + C content to that of the Brucella genome and is bounded by 20-bp imperfect inverted repeats (IR). The element appears to duplicate the nt TA of a consensus target site, YTAR (R, purines; Y, pyrimidines). When the complete nt sequence of four elements and 300 bp of the 3' ends of five other elements were compared to IS711 and to each other, minor nt sequence variations were found amongst most of them. Similar to several other transposable elements, IS711 has overlapping ORFs rather than one long ORF extending the length of the element. Even though only ten B. ovis IS711 elements were characterized, in three cases we found these elements flanked by either identical or similar nt sequences. This suggests that some target sites are hot spots for insertion and that some of the elements may be duplicated by mechanisms other than transposition. No DNA or protein database entries had an obvious resemblance to either IS711 or its deduced gene products.

Amino Acid Sequence↗
PubMed1987

Cloning and nucleotide sequence of different iso-IS231 elements and their structural association with the Tn4430 transposon in Bacillus thuringiensis.

A family of five repetitive sequences (RS) has been isolated from a plasmid DNA library of Bacillus thuringiensis strain berliner 1715. In a previous paper [Mahillon et al., EMBO J. 4(1985)3895-3899] one of these was shown to harbor all the features of an IS element (IS231). Further nucleotide sequence analysis revealed that two other RS, flanking the delta-endotoxin gene, are actually variants of IS231. Comparison of the nucleotide sequences surrounding the iso-IS231 elements showed a unique structural association between some of these elements and the transposon Tn4430. Although these IS231 elements have transposed into Tn4430, both these IS231 s and the transposon Tn4430 remain structurally intact.

Bacillus thuringiensis↗
PubMed2001

Tc8, a Tourist-like transposon in Caenorhabditis elegans.

Members of the Tourist family of miniature inverted-repeat transposable elements (MITEs) are very abundant among a wide variety of plants, are frequently found associated with normal plant genes, and thus are thought to be important players in the organization and evolution of plant genomes. In Arabidopsis, the recent discovery of a Tourist member harboring a putative transposase has shed new light on the mobility and evolution of MITEs. Here, we analyze a family of Tourist transposons endogenous to the genome of the nematode Caenorhabditis elegans (Bristol N2). One member of this large family is 7568 bp in length, harbors an ORF similar to the putative Tourist transposase from Arabidopsis, and is related to the IS5 family of bacterial insertion sequences (IS). Using database searches, we found expressed sequence tags (ESTs) similar to the putative Tourist transposases in plants, insects, and vertebrates. Taken together, our data suggest that Tourist-like and IS5-like transposons form a superfamily of potentially active elements ubiquitous to prokaryotic and eukaryotic genomes.

Amino Acid Sequence↗
PubMed2005

Allopolyploidy in wheat induces rapid and heritable alterations in DNA methylation patterns of cellular genes and mobile elements.

Whereas accumulating recent evidences indicate that allopolyploid formation in plants is accompanied by rapid and non-Mendelian genomic changes, some other works showed genomic stasis in both nascent and natural allopolyploids. To further study the issue, we performed global DNA fingerprinting of a newly synthesized allohexaploid wheat and its natural counterpart, the common wheat, by AFLP analysis. It was found that ca. 20% bands showed deviation from parental additivity in both synthetic and the natural common wheat. Sequence analysis indicates that a majority of the changed bands represent known-function genes and transposable elements. DNA gel blot analysis showed that the main type of changes in the amphiploid is epigenetic in nature, i.e., alteration in DNA methylation patterns. Two types of alterations in methylation, random and non-random, were detected, and both types were stably inherited. Possible causes and implications of the epigenetic changes in allopolyploid genome evolution and speciation are discussed.

DNA Methylation↗
PubMed2005

Characterization of the highly variable region surrounding the bla(CTX-M-9) gene in non-related Escherichia coli from Barcelona.

OBJECTIVES: The dispersion of a clone, a plasmid or a mobile element carrying the bla(CTX-M-9) gene was evaluated in 30 Escherichia coli strains isolated in Barcelona between 1996 and 1999. The presence of the previously described orf513-bearing class 1 integron, In60, carrying the bla(CTX-M-9) gene, was also studied. METHODS: The clonality was analysed by pulsed-field gel electrophoresis. Plasmid analysis was performed by S1 digestion and hybridization with the CTX-M-9 probe. PCR mapping using specific designed primers was used to study the presence of In60 and In60-like structures. RESULTS: The clonality between the 30 strains was minor. The size of bla(CTX-M-9) carrying plasmids ranged between approximately 80 and 430 kb. One strain produced only a chromosome-encoded CTX-M-9 beta-lactamase. Thirty-six per cent of the strains showed differences with respect to the In60 structure due to an insertion or deletion events. CONCLUSIONS: These findings suggest that the bla(CTX-M-9) gene may be carried by a mobile element that disperses it between plasmids. The fast dispersion of the CTX-M-9 enzyme could therefore be due to both diffusion of plasmids and mobile elements.

Base Sequence↗
PubMed1994

Developmentally regulated, low abundance Tec element transcripts in Euplotes crassus--implications for DNA elimination and transposition.

During macromolecular development in the ciliated protozoan, Euplotes crassus, > 105 Tec elements are precisely eliminated from the genome in a 2-4 h time interval, generating extrachromosomal circular forms of the elements. Various models have proposed a transposition-based mechanism for this excision. We have tested this hypothesis by determining the abundance of transcripts of Tec element open reading frames (ORFs) and the timing of their appearance. Transcripts are very low in abundance and are only detected by PCR amplification techniques. Thus, the low levels of transcripts argue against the participation of element-encoded functions in the Tec element elimination process. The element transcripts are only detected in RNA samples from mated cells, indicating that the micronucleus and/or developing macronucleus are transcriptionally active during the sexual phase of the life cycle. The transcription detected could allow a low level of germline-specific transposition for these elements.

Animals↗
PubMed2001

Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution.

Restriction-modification (RM) systems are composed of genes that encode a restriction enzyme and a modification methylase. RM systems sometimes behave as discrete units of life, like viruses and transposons. RM complexes attack invading DNA that has not been properly modified and thus may serve as a tool of defense for bacterial cells. However, any threat to their maintenance, such as a challenge by a competing genetic element (an incompatible plasmid or an allelic homologous stretch of DNA, for example) can lead to cell death through restriction breakage in the genome. This post-segregational or post-disturbance cell killing may provide the RM complexes (and any DNA linked with them) with a competitive advantage. There is evidence that they have undergone extensive horizontal transfer between genomes, as inferred from their sequence homology, codon usage bias and GC content difference. They are often linked with mobile genetic elements such as plasmids, viruses, transposons and integrons. The comparison of closely related bacterial genomes also suggests that, at times, RM genes themselves behave as mobile elements and cause genome rearrangements. Indeed some bacterial genomes that survived post-disturbance attack by an RM gene complex in the laboratory have experienced genome rearrangements. The avoidance of some restriction sites by bacterial genomes may result from selection by past restriction attacks. Both bacteriophages and bacteria also appear to use homologous recombination to cope with the selfish behavior of RM systems. RM systems compete with each other in several ways. One is competition for recognition sequences in post-segregational killing. Another is super-infection exclusion, that is, the killing of the cell carrying an RM system when it is infected with another RM system of the same regulatory specificity but of a different sequence specificity. The capacity of RM systems to act as selfish, mobile genetic elements may underlie the structure and function of RM enzymes.

Base Sequence↗
PubMed1992

Gene cassettes from the insert region of integrons are excised as covalently closed circles.

Integrons are DNA elements which generally include one or more discrete gene cassettes inserted at a specific site. We have recently proposed a model for the acquisition and dissemination of genes found in the insert region of integrons, which requires the existence of circularized gene cassettes. Evidence for the existence of covalently closed circular molecules consisting of one or more gene cassettes has now been obtained. Low levels of small molecules which hybridize to probes specific for individual gene cassettes were detected in plasmid DNA isolated from cells containing a plasmid which includes an integron fragment with three gene cassettes aacC1, orfE and aadA2. These molecules were only detected when the gene encoding the integron DNA integrase was also present and are thus products of site-specific cassette excision. The excised cassettes have been shown to be in the form of covalently closed supercoiled circles, by digestion with restriction enzymes exonuclease III and DNase I. The circular excision products detected included either one cassette, aadA2 or orfE, two cassettes, aacC1 and orfE or all three cassettes. The predicted sequence of the recombinant junction in the excised aadA2 cassette confirmed that excision was precise. The predicted unique sequences of the 59-base elements associated with individual genes in the circular cassette form were compiled, and the sequences of the seven-base core sites which flank 59-base elements are now, with few exceptions, exact inverted repeats.

Base Sequence↗
PubMed1983

Mapping of chromosomal IS5 elements that mediate type II F-prime plasmid excision in Escherichia coli K-12.

Three IS5 elements were mapped in overlapping chromosomal segments on a series of F-prime plasmids by restriction analysis and hybridization. IS5A was located clockwise of proA near 6 min, IS5B was located clockwise of purE near 12 min, and IS5C was tentatively located near 14 min on the Escherichia coli K-12 map. The physical structures of nine type II F-prime plasmids that contain chromosomal DNA from this region indicated that these plasmids were excised from the chromosome by recombination between pairs of IS5 elements.

Base Sequence↗
PubMed1984

Intrachromosomal movement of genetically marked Saccharomyces cerevisiae transposons by gene conversion.

In this paper, we describe the movement of a genetically marked Saccharomyces cerevisiae transposon. Ty912(URA3), to new sites in the S. cerevisiae genome. Ty912 is an element present at the HIS4 locus in the his4-912 mutant. To detect movement of Ty912, this element has been genetically marked with the S. cerevisiae URA3 gene. Movement of Ty912(URA3) occurs by recombination between the marked element and homologous Ty elements elsewhere in the S. cerevisiae genome. Ty912(URA3) recombines most often with elements near the HIS4 locus on chromosome III, less often with Ty elements elsewhere on chromosome III, and least often with Ty elements on other chromosomes. These recombination events result in changes in the number of Ty elements present in the cell and in duplications and deletions of unique sequence DNA.

DNA Transposable Elements↗