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Results for “DNA Transposable Elements”

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PubMed2004

A member of a repeat family is the source of an insertion-deletion polymorphism inside a developmentally eliminated sequence of Tetrahymena thermophila.

In Tetrahymena thermophila, the development of a transcriptionally active macronucleus from a transcriptionally inert micronucleus is accompanied by the elimination of numerous DNA segments, called internally eliminated sequences (IESs), many of which belong to dispersed repetitive sequence families. To examine the relationship between the insertion and deletion events expected to occur during evolution of the repeats and the developmental elimination process, IESs were compared among different Tetrahymena strains. A 600 base-pair DNA segment, the R Indel, was discovered inside the R IES, one of the ten sequenced IESs out of an estimated 6000 total in the Tetrahymena genome. The R Indel was found in strains B3 and C2 but not in several other strains examined, indicating that the Indel was probably present in a progenitor of strains B3 and C2. The R Indel was found to belong to a moderately large sequence family of about 200 members; however, BLAST searches did not reveal meaningful similarities with other mobile elements. Sequence comparisons revealed that a 300 base-pair stretch, very closely related to the first half of the R Indel, was present inside the previously described B IES, another of the ten sequenced IESs. This is the first example of shared sequences between two of the known IESs.

Animals↗

PubMed1997

Conservation of IS6110 sequence in strains of Mycobacterium tuberculosis with single and multiple copies.

The insertion sequence IS6110/IS986 is used extensively for detecting and typing Mycobacterium tuberculosis. In order to appreciate the evolutionary and epidemiological significance of differences in the fingerprint pattern, it is necessary to understand the factors influencing transposition frequency. Although most strains have many copies of this element, some have only one or two copies; it has been suggested that this apparent transpositional defect arises from the minor differences in the sequence of the element from different strains. In contrast, we have found that the sequence is identical in high and low copy number strains, indicating that external factors, such as the presence of adjacent promoters, must be responsible for differences in copy number.

Base Sequence↗

PubMed1992

The genetics of encapsulation in Haemophilus influenzae.

In Haemophilus influenzae type b (Hib) strains the cap locus with very few exceptions contains an unstable direct repeat of approximately 17 kb of DNA flanking an approximately 1-kb bridge region containing the gene bexA. Each repeat contains genes necessary for polysaccharide synthesis, export, and surface expression, with BexA a critical component of the polysaccharide exporter. Only rare Hib strains have been identified in which cap lacks a direct repeat, though this is the norm for non-b serotypes. Examination of the ends of this single-copy locus shows that cap has the structure of a compound transposon: Copies of the insertion element IS1016 flank the gene cluster. This gives strains the capacity to amplify genes at cap by unequal homologous recombination. The cap duplication in Hib strains--subserving augmented production of polysaccharide--has apparently arisen in this way and become fixed in the population through deletion of one copy of bexA.

Bacterial Capsules↗

PubMed1987

The yeast ROAM mutation--identification of the sequences mediating host gene activation and cell-type control in the yeast retrotransposon, Ty.

When the yeast retrotransposon, Ty, integrates into the 5' flanking region of a gene it can activate the expression of that gene. At the same time the activated gene is brought under cell-type specific control such that expression is high in haploid a or alpha cells but low in a/alpha diploids. These Ty mediated mutations are known as ROAM mutations. In this study we have used a ROAM mutation created in vitro to identify the sequences within Ty that mediate this phenomenon. We show that a single activator located within the coding region of the Ty element is responsible for ROAM activation. This sequence, which is regulated by the mating type of the cell, differs from classical enhancer elements in that its activity is strictly orientation dependent. An independent activator located downstream of the ROAM sequence activated transcription only in the non-ROAM orientation. This sequence may be part of an internal promoter that controls expression of the sub-genomic 5.0kb Ty transcript.

DNA Transposable Elements↗

PubMed2001

Evidence of recombination in Porphyromonas gingivalis and random distribution of putative virulence markers.

The association of Porphyromonas gingivalis to periodontal disease is not clearly understood. Similar proportions of P. gingivalis may be cultivated from both inactive and actively degrading periodontal pockets. Differences in virulence among strains of P. gingivalis exist, but the molecular reason for this remains unknown. We examined the population structure of P. gingivalis to obtain a framework in which to study pathogenicity in relation to evolution. Phylogenetic trees derived from the sequencing of fragments of four housekeeping genes, ahp, thy, rmlB, and infB, in 57 strains were completely different with no correlation between clustering of strains in the four dendrograms. Combining the various alleles of the four gene fragments sequenced resulted in 41 different sequence types. The index of association, I(A), based on a single representative of each sequence type was 0.143 +/- 0.202, indicating a population at linkage equilibrium. Inclusion of all isolates for the calculation of I(A) resulted in a value of 0.206 +/- 0.171. This suggests an epidemic population structure supported by the finding of genetically identical strains in different parts of the world. We observed a random distribution of two virulence-associated mobile genetic elements, the ragB locus and the insertion sequence IS1598, among 132 strains tested. In conclusion, P. gingivalis has a nonclonal population structure characterized by frequent recombination. Our study suggests that particular genotypes, possibly with increased pathogenic potential, may spread successfully in the human population.

Bacterial Proteins↗

PubMed1985

Structural and functional analyses of the fosfomycin resistance transposon Tn2921.

The fosfomycin resistance transposon Tn2921 is flanked by directly repeated sequences homologous to the Tn10-related insertion sequence IS10. The nonrepeated DNA sequences of Tn2921 can be deleted without affecting the transposition ability of the element, showing that at least one of the direct repeats is an active insertion sequence. Transposition of Tn2921 seems to occur through direct transposition, since cointegrates have not been observed. The evolutionary relatedness of Tn2921 and IS10 is discussed.

Anti-Bacterial Agents↗

PubMed1995

Reshuffling of Rhs components to create a new element.

RhsF has been identified as the fourth member of the RhsABCF subfamily of genetic elements. This new element is found in Escherichia coli ECOR-50 and several other strains but not in strain K-12. A novel feature of RhsF is that it represents a new arrangement of components previously uniquely associated with RhsA and RhsC of strain K-12.

Amino Acid Sequence↗

PubMed2002

Comparison of SXT and R391, two conjugative integrating elements: definition of a genetic backbone for the mobilization of resistance determinants.

The SXT element (SXT) is becoming an increasingly prevalent vector for the dissemination of antibiotic resistances in Vibrio cholerae. SXT is a member of a larger family of elements, formerly defined as IncJ plasmids, that are self-transmissible by conjugation and integrate site-specifically into the host chromosome. Comparison of the DNA sequences of SXT and R391, an IncJ element from Providencia rettgeri, indicate that these elements consist of a conserved backbone that mediates the regulation, excision/integration and conjugative transfer of the elements. Both elements have insertions into this backbone that either confer the element-specific properties or are of unknown function. Interestingly, the conserved SXT and R391 backbone apparently contains hotspots for insertion of additional DNA sequences. This backbone represents a scaffold for the mobilization of genetic material between a wide range of gram-negative bacteria, allowing for rapid adaptation to changing environments.

Base Sequence↗

PubMed2002

Mechanism of integration and excision in conjugative transposons.

Translocation of conjugative transposons proceeds via excision of the element to generate a circular molecule that can then integrate into a new site, which can be in the same or a different cell. This review summarises some of the different mechanisms used for excision and integration of conjugative transposons.

Bacteriophages↗

PubMed1996

Identification of a native Dichelobacter nodosus plasmid and implications for the evolution of the vap regions.

Studies on the role of various virulence factors of the ovine pathogen, Dichelobacter nodosus, have suffered from the absence of a mechanism for the introduction of DNA into this organism. As an initial step in the development of genetic methods, we have identified and cloned a native 10-kb plasmid, pJIR896, from a clinical isolate. This plasmid was found to be a circular form of vap region 1/3 that is found in the reference strain, A198. However, pJIR896 lacked the duplicated region present in the A198 sequence and instead contained a 1.7-kb putative insertion sequence, IS1253, which shared similarity to a number of unusual IS elements. A model is proposed for the evolution of vap region 1/3 which involves the integration of a plasmid, such as pJIR896, and subsequent rearrangements resulting from the deletion or transposition of IS1253.

Base Sequence↗

PubMed1994

Cloning of the nupC gene of Escherichia coli encoding a nucleoside transport system, and identification of an adjacent insertion element, IS 186.

Escherichia coli is known to contain more than one active transport system for nucleoside uptake. In the present study we report the sequence of a gene encoding a second nucleoside transport system, nupC (in addition to nupG). An open reading frame (ORF) of 1200 bp was identified that codes for a hydrophobic polypeptide of 43,560 Da and an NupC fusion protein was shown to be membrane associated. The native NupC protein is also identified, following over-expression. NupC exhibits short regions of homology to several membrane-associated proteins, including LacY and Cyd. Analysis of the nupC promoter region revealed the presence of at least two putative CRP-binding sites, centred at -40bp and -89bp, which probably flank a CytR-binding site. In addition, an adjacent IS 186 element was identified and found to reside within a putative terminator structure, downstream from the nupC ORF. This arrangement is shown to reflect the previously established gene order on the E. coli chromosome.

Amino Acid Sequence↗

PubMed1999

Characterization of a Mycobacterium bovis BCG insertion sequence related to the IS21 family.

The structure and distribution of a Mycobacterium bovis BCG insertion element of the IS21 family were investigated. Several IS21-like elements found in mycobacterial genomes were separated in four types, following their nucleic acid similarities. The M. bovis BCG IS21 element is highly similar to IS1533 (class I), 70% similar to IS1534 (class II), 52% similar to IS1532 (class III) of Mycobacterium tuberculosis, and 54% similar to both an Mycobacterium avium serovar 2 and an M. avium silvaticum IS (class IV). The M. bovis BCG IS21 element of the class I appears to be present in a single copy in the genome of M. bovis BCG, M. bovis, M. tuberculosis and Mycobacterium africanum and to be absent from all other tested species of the Corynebacteria-Mycobacteria-Nocardia group.

Amino Acid Sequence↗

PubMed2000

Local hopping of IS3 elements into the A+T-rich part of the high-pathogenicity island in Yersinia enterocolitica 1B, O:8.

The high-pathogenicity island (Yen HPI) of Yersinia enterocolitica biogroup (BG) 1B strains is associated with mouse virulence. Three repeated sequences are clustered on the A+T-rich part of the Yen HPI downstream of the fyuA yersiniabactin receptor gene in Y. enterocolitica O:8 strains WA-314 and 8081. In addition to IS1328 and IS1400, the RS3 repeated sequence consists of a novel insertion sequence, IS1329, inserted into the remnants of IS1222. This partial IS retains both 44-bp inverted terminal repeats (ITRs) of IS1222 but has suffered deletions of different sizes in strains WA-314 and 8081. IS1329 is 1243-bp long, carries 25-bp imperfect ITRs and two consecutive orfs capable to encode 110-amino acid (aa) and 249-aa proteins, respectively. IS1329 is present only in BG 1B Y. enterocolitica strains. Similarly to IS1400, IS1329 and IS1222 belong to the IS3 group of mobile elements and seem to have preference for the 'local hopping' into the A+T-rich part of the Yen HPI. These insertion sequences may be responsible for the imprecise deletions of the Yen HPI in strain WA-314.

AT Rich Sequence↗

PubMed2003

Transferable vanB2 Tn5382-containing elements in fecal streptococcal strains from veal calves.

Three vancomycin-resistant veal calf fecal streptococci, identified as Streptococcus gallolyticus (n = 2) and Streptococcus lutetiensis, were shown to harbor vanB2 Tn5382-like elements earlier described in enterococci. One S. gallolyticus strain had a 1,495-bp IS256-related element inserted in vanS(B). The vanB2 Tn5382 element present in the plasmid-free S. lutetiensis strain was transferable to Enterococcus faecium BM4105-RF, Enterococcus faecalis JH2-2, and its recombination-deficient derivative, UV202. The transfer frequencies were comparable between recipient strains (from 1 x 10(-7) to 7 x 10(-6)). All transconjugants acquired a vanB-containing chromosomal insert of approximately 100 kb, apparently by site-specific integration. Secondary transconjugants were not observed in intraspecies retransfer experiments. These observations are consistent with a conjugative, selftransmissible, integrative element that might be involved in the interspecies spread of vanB2 resistance determinants. Two JH2-2-derived transconjugants had also gained additional copies of large vanB-containing chromosomal fragments, a process that involves unexplained mechanisms that seems to require functional host cell-dependent recombination mechanisms.

Animals↗

PubMed1982

Construction of yeast strains containing genetically marked transposons.

Haploid yeast cells contain approximately 35 Ty (transposon yeast) elements. To facilitate the study of these elements, we have constructed yeast strains in which one of these transposons carries a genetic marker. The elements that we have modified are Ty912 and Ty917, elements originally detected at the HIS4 locus in spontaneously occurring his4- mutants. The strain constructions took place in three stages: 1) cloning of the mutant HIS4 genes containing the Ty elements; 2) introduction of a HindIII restriction fragment containing the yeast URA3 gene into the cloned transposons; and 3) replacement of the chromosomal HIS4 gene with the modified genes constructed in vitro. These strains will be extremely useful in the study of Ty transposition and other Ty-promoted DNA rearrangements.

Chromosomes↗

PubMed1985

Bombyx mori 28S ribosomal genes contain insertion elements similar to the Type I and II elements of Drosophila melanogaster.

We have examined the 28S ribosomal genes of the silkmoth, Bombyx mori, for the presence of insertion sequences. Two types of insertion sequences were found, each approximately 5 kb in length, which do not share sequence homology. Comparison of the nucleotide sequences of the junction regions with the uninserted gene reveals that one type of insertion has resulted in a 14 bp duplication of the 28S coding region at the insertion site. The location of this insertion and the 14 bp duplication are identical to that found in the Type I ribosomal insertion element of Drosophila melanogaster. The second type of insertion element is located at a site corresponding to approximately 75 bp upstream of the first type. The location of this insertion, the variability detected at its 5' junction, and a short region of sequence homology at its 3' junction suggest that it is related to the Type II element of D. melanogaster. This is the first example of a Type II-like rDNA insertion outside of sibling species of D. melanogaster, and the first example of a Type I-like rDNA insertion outside of the higher Diptera.

Animals↗

PubMed1994

Dissemination among staphylococci of DNA sequences associated with methicillin resistance.

DNA probes consisting of pUC19 containing cloned Staphylococcus aureus chromosomal fragments were constructed from two methicillin-resistant S. aureus strains with different DNA sequences 5' to mecA, the gene that mediates methicillin resistance. The probe from one strain, BMS1, contained a portion of the regulatory sequences (the terminal 641 bp of mecR1 and all of mecI) associated with the induction and repression of mecA transcription (pGO195). The second probe, from strain COL (pGO198), contained DNA not found in strain BMS1. This DNA was within the sequences added at the site of a mecR1 deletion. Genomic digests of 14 S. aureus isolates recovered between 1961 and 1969 all hybridized with pGO198. In contrast, 78% (36 of 46) of the S. aureus organisms isolated since 1988 hybridized with pGO195 but not with pGO198; the remainder hybridized with pGO198. No S. aureus isolates hybridized with both probes. Staphylococcus epidermidis digests hybridized with pGO198 (46%), pGO195 (14%), or both probes (35%); all 20 Staphylococcus haemolyticus isolates hybridized with pGO198. The restriction fragment length polymorphism patterns of all pGO198-hybridizing regions in S. aureus were identical to those in strain COL. In addition, the mecR1 deletion junction nucleotide sequences of eight S. aureus and six S. epidermidis isolates were identical. However, 21 of 23 S. epidermidis and all 20 S. haemolyticus isolates had from 5 to more than 20 additional chromosomal bands that hybridized with pGO198; none of 21 S. aureus isolates had additional hybridizing bands. These data suggest that the additional DNA responsible for the mecR1 deletion was part of a repetitive, and possibly mobile, element resident in coagulase-negative staphylococci but not in S. aureus. These data also support a hypothesis that the deletion event occurred in a coagulase-negative staphylococcus with subsequent acquisition of the interrupted sequences by S. aureus.

Base Sequence↗

PubMed1994

[Tv1--a new family of Drosophila virilis retrotransposons].

A new method for isolation and cloning of functionally active retrotransposons was proposed and tested. The method is based on the hypothesis about the universal character of retrotransposition through reverse transcription. A new retrotransposon family (Tvl) was coned from the Drosophila virilis genome. A full-length Tvl copy was 7 kb. The cell line under consideration contained 500-1000 Tvl copies per cell, i.e., it accounted for 0.3% of the genome. Tvl RNA, detected in the cell culture, was almost absent in cells of adult flies. A 7-kb polyadenylated RNA was the main transcript of Tvl. Extrachromosomal circular and linear Tvl copies were cloned and characterized. The following features of Tvl structural organization were studied: (1) element was flanked by perfect direct repeats of 453 bp size (long terminal repeats, LTRs); (2) element sequences adjacent to the LTRs were homologous to binding sites of primer serine tRNA and the polypurine blocks of retrotransposons 17.6 and 297; and (3) expected transcription of LTRs occurred as for known retrotransposons, --producing RNA with a direct terminal repeat.

Animals↗