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Results for “DNA Transposable Elements”

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PubMed1999

Stability of insertion sequence IS1245, a marker for differentiation of Mycobacterium avium strains.

Recently a novel insertion element, IS1245, has been described and suggested for use as a probe in restriction fragment length polymorphism studies of Mycobacterium avium strains. An important issue in this context is the stability of the insertion element. We analyzed single colonies of M. avium cultures and found frequent small one- to two-band changes. However, following repeated in vitro passages over 1 year, similar one- to two-band changes were observed in the IS1245 patterns of only six M. avium strains investigated.

AIDS-Related Opportunistic Infections↗

PubMed2006

The DcMaster Transposon Display maps polymorphic insertion sites in the carrot (Daucus carota L.) genome.

DcMaster is a family of PIF/Harbinger-like class II transposable elements identified in carrot. We present a modified Transposon Display molecular marker system allowing amplification of genomic regions containing DcMaster elements. We scored 77 DcMaster Transposon Display (DcMTD) amplicons, of which 54 (70%) were segregating in the F(2) progeny from the cross between wild and cultivated carrot. Segregating amplicons were incorporated into a previously developed molecular linkage map of carrot. Twenty-eight markers were attributed to the wild parent, 23 originated from the cultivated parent, and three markers remained unlinked. The markers were evenly distributed among the nine linkage groups. However, differences in the distribution pattern of DcMaster insertion sites in the genomes of the wild and cultivated parent were observed. Specificity of the obtained amplicons was confirmed by sequencing and three putative DcMaster subfamilies, differing in the sequence of their terminal inverted repeats, were revealed.

Base Sequence↗

PubMed1998

A flax transposon identified in two spontaneous mutant alleles of the L6 rust resistance gene.

Two spontaneous mutant alleles of the L6 flax rust resistance gene, 16-X3A and 16-X117, contain the same transposable element designated dLute (defective Linum usitatissimum transposable element). The element is 314 bp long, 70% AT-rich and, because it contains no extended open reading frame, is probably non-autonomous. It has 14 bp imperfect terminal inverted repeats related to those in the Ac family of plant transposons and, like Ac, causes 8 bp target site duplications upon insertion. Multiple copies of dLute-related sequences exist in the flax genome. Rust resistant revertants were recovered amongst the progeny of both mutants and reversion was associated with excision of dLute. Excision either restored the wild-type L6 sequence or was imprecise, leaving sequence alterations ('footprints') resulting in one to three amino acid alterations in the L6 protein. No phenotypic differences were discerned between plants containing the standard and revertant L6 alleles.

Alleles↗

PubMed1996

PCR analysis of insertion site specificity, transcription, and structural uniformity of the Lepidopteran transposable element IFP2 in the TN-368 cell genome.

The IFP2 element is a unique Lepidopteran transposon that has been associated with spontaneous Baculovirus mutants isolated following passage of the virus in the TN-368 cell line. Independent genomic representatives of IFP2 from TN-368 cells show little sequence divergence, suggesting that IFP2 was recently introduced into this genome and is highly stable. IFP2 is inserted within AT-rich regions of the TN-368 genome and targets TTAA sites. The specificity for TTAA target sites during transposition is not limited to the movement of IFP2 during an active Baculovirus infection, but is a property of its movement in uninfected cells as well. The exact origin of IFP2 remains obscure since it is found in two independently established Trichoplusia ni cell lines but not in three others, and we have not yet identified any IFP2 sequences in either field collected larvae or laboratory colonies.

Animals↗

PubMed1993

Shuttle mutagenesis: two mini-transposons for gene mapping and for lacZ transcriptional fusions in Neisseria gonorrhoeae.

Shuttle mutagenesis is a system we developed for producing stable transposon insertions in Saccharomyces cerevisiae [Seifert et al., Proc. Natl. Acad. Sci. USA 83 (1986) 735-739; Hoekstra et al., Methods Enzymol. 194 (1991) 329-342] and Neisseria gonorrhoeae (Gc) [Seifert et al., J. Bacteriol. 172 (1990) 40-46] by transposition in Escherichia coli and transformation into yeast or Gc. In developing the system for use in Gc, a series of mini-transposons (mTn) were derived from mTn3 which confer resistance to chloramphenicol in Gc (mTnCm) (Seifert et al., 1990). Herein, we describe the creation of two mTnCm derivatives for use in Gc. One of these transposons, mTnCmNS, contains the infrequently occurring NheI and SpeI restriction sites to localize genes on the gonococcal macro-restriction map which was recently developed using these restriction sites [Bihlmaier et al., Mol. Microbiol. 5 (1991) 2529-2539; Dempsey et al., J. Bacteriol. 173 (1991) 5476-5486]. The mTnCmLac was developed to generate lacZ transcriptional fusions using transposition. It contains at its end a promoterless lacZ gene which is expressed once the element has transposed downstream from a promoter in a cloned gene. In adapting the use of mTnCmLac to the shuttle mutagenesis system, we have identified some factors which affect the transformation of Gc using cloned chromosomal fragments containing the large heterologous insertion, mTnCmLac. Using mTnCmLac, we have created Gc variants containing a pilE::mTnCmLac fusion to determine that pilE transcription in Gc is not auto-regulated.

Base Sequence↗

PubMed1992

Selective detection of Mycoplasma fermentans by polymerase chain reaction and by using a nucleotide sequence within the insertion sequence-like element.

A new assay using the polymerase chain reaction to amplify a 206-nucleotide specific gene sequence within the insertion sequence-like element of Mycoplasma fermentans has been developed. The unique insertion sequence-like element exists in multiple copies in the M. fermentans genome. The assay selectively amplifies DNA from all strains of M. fermentans tested. In contrast, DNA from other species of human and nonhuman mycoplasmas, common tissue culture-contaminating mycoplasmas, and bacteria, as well as human, monkey, and mouse tissues do not produce the amplified DNA products specific for M. fermentans.

Animals↗

PubMed1985

Recombination sites in plasmid drug resistance gene amplification.

The resistance plasmid NR1 derivative pRR330 consists of a neomycin-kanamycin resistance gene (neo-kan) flanked by directly repeated sequences of both insertion element IS1 DNA (768 base pairs) and 840 base pairs of DNA which are a part of the chloramphenicol acetyltransferase (cam) gene. Most Escherichia coli cell populations that were cultured in high neomycin concentrations carried plasmids whose neo-kan gene amplification was mediated either by IS1 DNA or by cam DNA as homologous recombination sites. This suggests that the final amplified cell populations were the descendants of a single cell.

DNA Restriction Enzymes↗

PubMed1988

Tn4201, a beta-lactamase transposon in Staphylococcus aureus.

We report the preliminary characterization of a 6.7-kilobase transposon, Tn4201, encoding resistance to penicillin associated with the conjugative plasmid pCRG1600 in Staphylococcus aureus. Tn4201 is capable of inverting in orientation (frequently observed in derivatives of pCRG1600) and is expressed equally well in either orientation. The element is also capable of movement to alternative plasmid and chromosomal sites. Tn4201 exhibits rec-independent transposition in an apparent site-specific manner and may play an important role in the resistance of staphylococci to beta-lactam compounds.

Anti-Bacterial Agents↗

PubMed2005

Transcribed Tc1-like transposons in salmonid fish.

BACKGROUND: Mobile genetic elements comprise a substantial fraction of vertebrate genomes. These genes are considered to be deleterious, and in vertebrates they are usually inactive. High throughput sequencing of salmonid fish cDNA libraries has revealed a large number of transposons, which remain transcribed despite inactivation of translation. This article reports on the structure and potential role of these genes. RESULTS: A search of EST showed the ratio of transcribed transposons in salmonid fish (i.e., 0.5% of all unique cDNA sequences) to be 2.4-32 times greater than in other vertebrate species, and 68% of these genes belonged to the Tc1-family of DNA transposons. A phylogenetic analysis of reading frames indicate repeated transposition of distantly related genes into the fish genome over protracted intervals of evolutionary time. Several copies of two new DNA transposons were cloned. These copies showed relatively little divergence (11.4% and 1.9%). The latter gene was transcribed at a high level in rainbow trout tissues, and was present in genomes of many phylogenetically remote fish species. A comparison of synonymous and non-synonymous divergence revealed remnants of divergent evolution in the younger gene, while the older gene evolved in a neutral mode. From a 1.2 MB fragment of genomic DNA, the salmonid genome contains approximately 10(5) Tc1-like sequences, the major fraction of which is not transcribed. Our microarray studies showed that transcription of rainbow trout transposons is activated by external stimuli, such as toxicity, stress and bacterial antigens. The expression profiles of Tc1-like transposons gave a strong correlation (r2 = 0.63-0.88) with a group of genes implicated in defense response, signal transduction and regulation of transcription. CONCLUSION: Salmonid genomes contain a large quantity of transcribed mobile genetic elements. Divergent or neutral evolution within genomes and lateral transmission can account for the diversity and sustained persistence of Tc1-like transposons in lower vertebrates. A small part of transposons remain transcribed and their transcription is enhanced by responses to acute conditions.

Amino Acid Sequence↗

PubMed1998

Genetic diversity among Mycobacterium avium complex strains recovered from children with and without human immunodeficiency virus infection.

The genetic diversity and molecular epidemiology of Mycobacterium avium complex (MAC) infections in children with and without human immunodeficiency virus (HIV) infection were evaluated. Isolates recovered from 136 children were subtyped by sequence analysis of a 360-bp region of the gene (hsp65) encoding a 65-kDa heat-shock protein. Twenty-one distinct hsp65 alleles were identified. On the basis of hsp65 genotype, 6 isolates were not MAC organisms. Of the remaining 130 samples, 61% were M. avium, 37% were Mycobacterium intracellulare, and 2% were species nonspecific MAC. Eighty-eight percent of the isolates obtained from HIV-infected children were M. avium. In contrast, only 38% of the isolates obtained from children without HIV infection were M. avium (chi2 test, P < .001). M. avium isolates were further subtyped by Southern blot analysis with insertion element IS1245. Taken together, no evidence for a single clonal M. avium strain causing infection was detected.

AIDS-Related Opportunistic Infections↗

PubMed1992

Natural occurrence of structures in oral streptococci and enterococci with DNA homology to Tn916.

Seventeen oral streptococci and 18 enterococci were tested for the presence of DNA sequences homologous to the conjugative transposon Tn916 encoding tetracycline resistance. All the strains were resistant to tetracyclines, including minocycline, and most of them were resistant to other antibiotics. Tn916-like structures, identified by hybridization of HincII-digested DNA, were found on the chromosomes of 11 oral streptococci and four enterococci and on two plasmids, pIP1549 and pIP1440, one harbored by an Enterococcus hirae strain and the other harbored by an Enterococcus faecalis strain. Sequences homologous to Tn916, only some of which corresponded to its internal HincII structure (Tn916-modified elements), were chromosomally located in three oral streptococci and two enterococci and were plasmid borne in pIP614 harbored by an E. faecalis strain. Nine enterococci and three oral streptococci carried either the Tet M or the Tet O determinant chromosomally, but they carried no other sequences homologous to Tn916.

Anti-Bacterial Agents↗

PubMed1997

Neuropeptide amidation in Drosophila: separate genes encode the two enzymes catalyzing amidation.

In vertebrates, the two-step peptide alpha-amidation reaction is catalyzed sequentially by two enzymatic activities contained within one bifunctional enzyme called PAM (peptidylglycine alpha-amidating mono-oxygenase). Drosophila head extracts contained both of these PAM-related enzyme activities: a mono-oxygenase (PHM) and a lyase (PAL). However, no bifunctional PAM protein was detected. We identified cDNAs encoding an active mono-oxygenase that is highly homologous to mammalian PHM. PHM-like immunoreactivity was found within diverse larval tissues, including the CNS, endocrine glands, and gut epithelium. Northern and Western blot analyses demonstrate RNA and protein species corresponding to the cloned PHM, but not to a bifunctional PAM, leading us to predict the existence of separate PHM and PAL genes in Drosophila. The Drosophila PHM gene displays an organization of exons that is highly similar to the PHM-encoding portion of the rat PAM gene. Genetic analysis was consistent with the prediction of separate PHM and PAL gene functions in Drosophila: a P element insertion line containing a transposon within the PHM transcription unit displayed strikingly lower PHM enzyme levels, whereas PAL levels were increased slightly. The lethal phenotype displayed by the dPHM P element insertion indicates a widespread essential function. Reversion analysis indicated that the lethality associated with the insertion chromosome likely is attributable to the P element insertion. These combined data indicate a fundamental evolutionary divergence in the genes coding for critical neurotransmitter biosynthetic enzymes: in Drosophila, the two enzyme activities of PAM are encoded by separate genes.

Amides↗

PubMed1983

Amplification of rDNA and type I sequences in Drosophila males deficient in rDNA.

rDNA magnification is a heritable change in rDNA content that occurs in D. melanogaster males when chromosomes deficient in rDNA are placed together for several generations. We have examined the restriction endonuclease cleavage pattern of the rDNA from an X chromosome undergoing magnification, and find no evidence for the selective amplification of either uninterrupted rDNA units or those containing insertion sequences. In addition, we observe an amplification of rDNA in the first generation of extremely bobbed male progeny to a level exceeding that of wild-type flies, but that reduces to the wild-type level in subsequent generations. The type I rDNA insertion elements also occur as tandem arrays, independently of rDNA. Southern hybridizations indicate that the majority of these sequences are located in the heterochromatin surrounding the nucleolus organizer on the X chromosome, and we find that they, too, amplify transiently in the first generation of magnifying males.

Animals↗

PubMed1993

Identification of a cryptic gene associated with an insertion sequence not previously identified in Bacillus thuringiensis.

After screening several Bt strains with a cryII toxin probe, clones from two strains were found to contain a cryptic cryIIB gene associated with an insertion sequence element belonging to the IS2/IS3 family. The lack of expression of this gene appears to result from mutation of the upstream orf2 gene which has been shown to be necessary for cryII expression.

Amino Acid Sequence↗

PubMed1993

Analysis of a viral integration event in a CG-rich region at the 1p36 human chromosomal site.

The preinsertion site of an adenovirus-5/simian virus 40 recombinant construct (Ad5/SV40) has been cloned and sequenced. Our data suggest that viral integration has occurred in a genomic region which has been the target of multiple events of Alu element retropositions within a TAA minisatellite. Extensive homologies between the left viral end and the host cellular DNA were also observed. The compositional similarity between Adenoviridae and the region of viral integration is consistent with the observed insertion of exogenous DNA in isochores of similar composition [G. Bernardi, Annu. Rev. Genet. 23 (1989) 637-661].

Base Sequence↗

PubMed1997

Structure and function of 59-base element recombination sites associated with mobile gene cassettes.

The integration of gene cassettes into integrons is effected by site-specific recombination catalysed by an integrase, IntI, encoded by the integron. The cassette-associated recombination sites, 59-base elements, are not highly conserved and vary in length from 57 to 141 bp. They can be identified by their location and the relationship of over 20 bp at their outer ends to consensus sequences that are imperfect inverted repeats of one another. The recombination cross-over occurs close to one end of the 59-base element, within a conserved core site with the consensus sequence GTTAGGC or GTTRRRY. By introducing single-base changes at each of these positions in the aadB 59-base element, bases that are critical for site activity were identified. The recombination cross-over was also localized to a unique position between the adjacent G and T residues. Changes introduced in the conserved AAC of the inverse core site (GCCTAAC or RYYYAAC) located at the opposite end of the 59-base element also reduced site activity but to a lesser extent. Sequences of rare recombinants revealed an alternative position for strand exchange and led to the conclusion that 59-base elements comprise two simple sites, analogous to those recognized by other integrases, with each simple site made up of a pair of inversely oriented IntI binding domains separated by a spacer of 7 or 8 bp. Re-examination of the sequences of all known 59-base elements revealed that this simple site configuration was present at both the left and right ends in all 59-base elements. The identity of bases in the spacer is not required for efficient recombination and the cross-over is located at one end of the spacer, suggesting that during IntI1-mediated recombination only one strand exchange occurs.

Base Composition↗

PubMed1996

Rho-dependent termination of transcription is governed primarily by the upstream Rho utilization (rut) sequences of a terminator.

A Rho-dependent transcription terminator in Escherichia coli DNA consists of an upstream part for Rho utilization (rut) and the transcription stop point (tsp) region. To test the role of the tsp region variants of the coliphage lambda cro gene terminator, tR1, containing inserts of non-terminator sequences between its rut and tsp regions were tested for termination function. The results showed that termination occurred with high efficiency at multiple sites in each of the new sequences with the positions of the sites coinciding with transcriptional pause points in the insert sequence and that the efficiency of termination was not directly proportional to the extent of pausing at those points. Thus, in contrast to the rut sequences, which are relatively rare in DNA, many different sequence segments can function as a tsp region. Studies with isolated transcripts showed that a rut element and sequences 3' of the rut element were both needed to activate ATP hydrolysis by Rho factor with the degree of activation depending on the length and the specific sequence of the 3' segment. These results support models for Rho action in which ATP hydrolysis is coupled to interactions of Rho protein with RNA 3' of the rut region.

Adenosine Triphosphatases↗

PubMed1985

Insertion of a long KpnI family member within a mitochondrial-DNA-like sequence present in the human nuclear genome.

Structural analysis of a phage lambda Charon 4A clone carrying one of the human nuclear mitochondrial(mut)-DNA-like sequences revealed that a KpnI-family member (KpnI 5.5-kb DNA) is inserted within this sequence. The inserted KpnI 5.5-kb DNA contains several possible polyadenylation signal sequences followed by an A-rich sequence at its 3' end and is flanked by perfect 13-bp direct repeats of the duplicated mtDNA-like sequences. These structures strongly suggest that the KpnI 5.5-kb DNA is a mobile element. Comparison of the 5' terminal sequences of the KpnI 5.5-kb DNA and four other long KpnI-family DNAs so far examined, using the predicted general promoter sequence for eukaryotic tRNAs, indicates that they contain the consensus sequences for the split internal RNA polymerase III control region.

Base Sequence↗