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At least 397 records · Page 22Linked to original sources
PubMed1998

Locus-specific diagnostic tests for endogenous avian leukosis-type viral loci in chickens.

The genome of the chicken, Gallus gallus, contains endogenous proviral elements (ALVE elements or ev genes) that display a high degree of similarity to the Avian Leukosis class of retroviruses. The ALVE proviruses are known to modulate physiological processes of the host birds. Different ALVE elements retain variable portions of the complete, prototype viral genome, and each provirus resides in its own specific location within the host genome. Thus, each ALVE element has its own particular potential to modulate host physiology depending on the nature of its integration site, the completeness of the proviral genome, and the level of expression of the locus. It is important, therefore, to be able to establish the ALVE element profiles of chickens quickly and accurately, both in the laboratory and in a commercial setting. The current method of choice for simple, quick, and accurate typing is the polymerase chain reaction (PCR). This paper reviews the present status of PCR typing of ALVE proviruses and lists the assay protocols for 19 different elements. In addition, it compares the insertion sites of these elements in an effort to identify common motifs at ALVE integration sites.

Animals↗
PubMed1994

Insertions of IS256-like element flanking the chromosomal beta-lactamase gene of Enterococcus faecalis CX19.

We have previously identified an inverted repeat characteristic of staphylococcal beta-lactamase transposons adjacent to the chromosomal beta-lactamase genes of Enterococcus faecalis CH19 and its beta-lactamase-producing transconjugant CX19. Nucleotide sequence analysis of the CH19 beta-lactamase structural gene (blaZ) reveals it to be identical to the blaZ gene from E. faecalis HH22 and to the blaZ gene from the staphylococcal beta-lactamase transposon Tn552. We also report the presence of nucleotide sequence identical to a 317-bp region of the staphylococcal insertion sequence IS256 upstream of the blaZ gene in both CH19 and CX19. The identical segment of IS256 is present downstream of the blaZ gene of CX19, suggesting a second insertion of the element (in the inverted orientation) accompanying transfer to the recipient strain. Restriction analysis of the areas beyond the ClaI sites used to clone these regions suggests that full copies of the IS256-like element (designated IS256E) are present in all positions but that these elements were not directly involved in the transfer of the beta-lactamase gene to the recipient strain. We have also identified a region downstream of the second IS256E insertion site which exhibits substantial homology to ISSIW, an iso-ISSI insertion originally identified in Lactococcus lactis subsp. cremoris. These data suggest that the two enterococcal blaZ genes sequenced to date evolved from a common ancestor and may at one time have been incorporated into a transposon similar to Tn552. They also suggest that IS256-like elements are mobile in E. faecalis and capable of inserting in a manner consistent with the formation of novel composite transposons. Finally, they provide the first confirmation of the presence of an ISSI-like element in enterococci, raising the possibility that these elements play a role in the exchange of chromosomal antimicrobial resistance determinants.

Base Sequence↗
PubMed2001

Rapid screening technique for class 1 integrons in Enterobacteriaceae and nonfermenting gram-negative bacteria and its use in molecular epidemiology.

A screening technique for integrons in members of the family Enterobacteriaceae and nonfermenting gram-negative bacteria by real-time PCR is reported. A total of 226 isolates of gram-negative bacteria obtained from a variety of clinical specimens were screened for class 1 integrons by real-time PCR performed on a LightCycler instrument. This technique used a primer pair specific for a 300-bp conserved region at the 5' ends of class 1 integrons. The screening assay was evaluated by comparison with results obtained by the conventional, thermal-block PCR (long PCR) by using established conditions and primers for the detection of class 1 integrons, and the real-time PCR technique was thus shown to be both sensitive and specific. DNA from 50 of 226 (22%) isolates screened was identified as containing an integron by the screening PCR, and sequence data were obtained across the integron for 34 of 50 (68%) of these isolates. In an attempt to study the molecular epidemiology of antimicrobial resistance genes carried within integrons, a comparison of the types of gene cassettes carried by isolates from different patients was made. Adenyltransferase genes conferring resistance to streptomycin and spectinomycin were the predominant gene cassettes amplified in the study. Resistance to trimethoprim was also frequently found to be encoded within integrons. Furthermore, multiple bacterial isolates obtained from one patient over a 5-month period were all shown to carry an integron containing the same single adenyltransferase gene cassette, suggesting that these elements were relatively stable in this case.

Community-Acquired Infections↗
PubMed1990

Insertion elements on lactococcal proteinase plasmids.

DNA segments of 809 and 808 nucleotides, with 18-base-pair terminal inverted repeats, are present on the proteinase plasmids pWV05 from Lactococcus lactis subsp. cremoris Wg2 and pSK111 from L. lactis subsp. cremoris SK11, respectively. These DNA segments are highly similar: 77% identical nucleotides and both contain an open reading frame that can encode a protein of 226 amino acids. Furthermore, both DNA segments are located downstream of the proteinase maturation gene prtM, but they differ individually in their orientation with respect to the prtM gene. On the basis of the striking similarity between ISS1, an 808-base-pair insertion sequence (IS) from L. lactis subsp. lactis ML3 lactose plasmid pSK08, and the DNA segments of pWV05 and pSK111, we propose that these DNA segments comprise IS elements. The IS elements from strains Wg2 and SK11 were named ISS1W and ISS1N, respectively. On pWV05, ISS1W is flanked on one side by only part of a second IS element, indicating that pWV05 evolved as a deletion derivative of a precursor plasmid that carried at least two IS elements.

Amino Acid Sequence↗
PubMed1991

An Acetobacter xylinum insertion sequence element associated with inactivation of cellulose production.

An insertion sequence (IS) element, IS1031, caused insertions associated with spontaneous cellulose deficient (Cel-) mutants of Acetobacter xylinum ATCC 23769. The element was discovered during hybridization analysis of DNAs from Cel- mutants of A. xylinum ATCC 23769 with pAXC145, an indigenous plasmid from a Cel- mutant of A. xylinum NRCC 17005. An IS element, IS1031B, apparently identical to IS1031, was identified on pAXC145. IS1031 is about 950 bp. DNA sequencing showed that the two elements had identical termini with inverted repeats of 24 bp containing two mismatches and that they generated 3-bp target sequence duplications. The A. xylinum ATCC 23769 wild type carries seven copies of IS1031. Southern hybridization showed that 8 of 17 independently isolated spontaneous Cel- mutants of ATCC 23769 contained insertions of an element homologous to IS1031. Most insertions were in unique sites, indicating low insertion specificity. Significantly, two insertions were 0.5 kb upstream of a recently identified cellulose synthase gene. Attempts to isolate spontaneous cellulose-producing revertants of these two Cel- insertion mutants by selection in static cultures were unsuccessful. Instead, pseudorevertants that made waxlike films in the liquid-air interface were obtained. The two pseudorevertants carried new insertions of an IS1031-like element in nonidentical sites of the genome without excision of the previous insertions. Taken together, these results suggest that indigenous IS elements contribute to genetic instability in A. xylinum. The elements might also be useful as genetic tools in this organism and related species.

Base Sequence↗
PubMed1994

Mycobacterium smegmatis strain for detection of Mycobacterium tuberculosis by PCR used as internal control for inhibition of amplification and for quantification of bacteria.

For the detection of Mycobacterium tuberculosis by PCR, the IS6110 sequence was used. A modified target was constructed by insertion of 56 nucleotides in the IS6110 insertion element of Mycobacterium bovis BCG. This modified insertion sequence was integrated into the genome of Mycobacterium smegmatis, a mycobacterium species which does not contain the IS6110 element. When DNA from the modified M. smegmatis 1008 strain was amplified with IS6110-specific primers INS1 and INS2, a band of 301 bp was seen on agarose gel, whereas the PCR product of M. tuberculosis complex DNA was a 245-bp fragment with these primers. The addition of a small number of M. smegmatis 1008 cells to clinical samples before DNA purification enables the detection of problems which may be due to the loss of DNA in the isolation procedure or to the presence of inhibitors. The presence of inhibitors of the amplification reaction can be confirmed by the addition of M. smegmatis 1008 DNA after the DNA isolation procedure. Furthermore, competition between the different target DNAs of M. smegmatis 1008 DNA and M. tuberculosis complex DNA enables the estimation of the number of IS6110 elements in the clinical sample.

Base Sequence↗
PubMed1988

The distribution of P elements in D. melanogaster along the coast of China studied by DNA hybridization method.

The distribution of the P-M system in four local Drosophila melanogaster populations obtained in southern China has been examined by mating tests. There was no P strain. A HindIII fragment of the P element has been cloned, named as pPH 0.86, and used as probe in this study. The distribution of the P element itself in thirteen local D. melanogaster populations along the eastern coast of China has been studied by the method of DNA hybridization. It is found that all the populations obtained from the north of Shanghai carry P elements but few populations from the south of Shanghai carry P elements. In comparison with the mating test, the method of DNA hybridization is more direct and reliable. The origin and trends of distribution of P elements in China are discussed in this paper.

Animals↗
PubMed2001

Transposition of IS10 from the host Escherichia coli genome to a plasmid may lead to cloning artefacts.

During recloning of Nicotiana tabacum L. repetitive sequence R8.3 in Escherichia coli, a modified clone that differed from the original by the insertion of an IS10 sequence was unintentionally produced. The insert was flanked by a 9-bp direct repeat derived from the R8.3 sequence, the 9-bp duplication of acceptor DNA in the site of insertion being a characteristic of IS10 transposition events. A database search using the FASTA program showed IS10 and other prokaryotic IS elements inserted into numerous eukaryotic clones. Unexpectedly, the IS10, which is not a natural component of the E. coli genome, appeared to be by far the most frequent contaminant of DNA databases among several IS sequences tested. In the GenEMBL database, the IS10 query sequence yielded positive scores with more than 500 eukaryotic clones. Insertions of shortened IS10 sequences having only one intact terminal inverted repeat were commonly found. Most full-length IS10 insertions (32 out of 40 analyzed) were flanked by 9-bp direct repeats having the consensus 5'-NPuCNN-NGPyN-3' with a strong preference for 5'-TGCTNA-GNN-3'. One insertion was flanked by an inverted repeat of more than 400 bp in length. PCR amplification and Southern analysis revealed the presence of IS10 sequences in E. coli strains commonly used for DNA cloning, including some reported to be Tn10-free. No IS10-specific PCR product was obtained with N. tabacum or human DNA. Our data suggest that transposition of IS10 elements may accompany cloning steps, particularly into large BAC vectors. This might lead to the relatively frequent contamination of DNA databases by this bacterial sequence. It is estimated that one in approximately every thousand eukaryotic clone in the databases is contaminated by IS-derived sequences. We recommend checking submitted sequences for the presence of IS10 and other IS elements. In addition, DNA databases should be corrected by removing contaminating IS sequences.

Animals↗
PubMed1987

Identification and nucleotide sequence of the regions of Autographa californica nuclear polyhedrosis virus genome carrying insertion elements derived from Spodoptera frugiperda.

A morphology mutant of the baculovirus Autographa californica nuclear polyhedrosis virus called M5 was previously shown to synthesize two size classes of viral DNA, one of which had a deletion of 42% of the genome. It was hypothesized that the presence of the smaller M5 circular DNA resulted from the specific deletion of the region located between two sites carrying short DNA insertions. These sites have now been identified by DNA-DNA hybridization using cloned EcoRI fragments of M5 DNA. One cloned M5 EcoRI fragment was found to correspond to the deletion junction fragment where sequences from the insertion site in the 2.6-map unit region were covalently linked to sequences from the insertion site in the 46-map unit region. The 2.6- and 46-map unit regions of Wt AcMNPV DNA were sequenced. Potential long open reading frames which would be disrupted by the M5 inserts were detected. Nucleotide sequence analysis of the same regions of M5 DNA revealed the presence of almost identical inserts of 290 bp. The primary sequence of the inserts revealed characteristics similar to the termini of transposons. Hybridization studies suggested that the inserts were derived from repetitive elements of the Spodoptera frugiperda host cell genome.

Animals↗
PubMed1992

Interaction of H-2Eb with an IAP retrotransposon in the A20/2J B cell lymphoma.

In the A20/2J BALB/c B cell lymphoma, Southern analysis revealed an insertion of approximately 6 kilobases of DNA into the first intron of one Ebd-allele. Two observations suggest that the rearrangement did not occur recently in the A20/2J subline. Firstly, normal and altered Ebd-alleles are present in equal numbers, and secondly, the LB 27.4 and LS 102.9 somatic cell hybrids formed at an earlier date both possess the rearrangement. Sequences of two cDNA clones, lambda Eb-7 and lambda Eb-125, selected from an A20/2J cDNA library prepared from poly [A+] RNA indicate that the rearranged Ebd-allele directs the synthesis of atypical Eb transcripts. The clones contain Eb sequence linked to a portion of retroviral-like intracisternal A-particle (IAP) genomic sequence, and they appear to be copies of mRNA produced by splicing between a 5' donor site in the retroviral transcript and the 3' acceptor site of the Eb gene's first intron. The longer lambda Eb-125 insert corresponds to RNA that initiated in the 5'-untranslated region of the Eb gene. The 3'-end of the first Eb exon joins to long terminal repeat sequence, and retroviral sequence extends up to the splice junction with the second Eb exon; 3' of the junction, the lambda Eb-125 sequence corresponds to that of a correctly spliced Eb transcript. It seems feasible that the cDNA clones represent hybrid RNA synthesized by read-through transcription of the Eb coding region and an IAP element inserted into the first intron of the rearranged Ebd-allele.

Animals↗
PubMed2005

Anaconda, a new class of transposon belonging to the Mu superfamily, has diversified by acquiring host genes during rice evolution.

A new type of transposon, named Anaconda (Anac) has been found in rice (Oryza sativa). In this paper, we demonstrate that Anaconda elements have diversified by acquisition of host cellular genes, amplification of the elements, and substitution and deletion of short segments. We identified four Anaconda elements in studies of rice alternative oxidase (AOX) genes, and subsequently isolated an additional 23 elements based on the identity of their terminal inverted repeats (TIRs). The Anaconda elements have long TIRs (114-458 bp). They also have direct repeats of 9 or 10 bp in their flanking regions that are thought to have been generated upon transposition. These structural features reveal that the Anaconda elements belong to the Mu superfamily. The most prominent feature of the Anaconda elements is the high frequency with which they have acquired host cellular genes. Of the 27 elements found here, 19 appear to have sequences presumably derived from rice genes, for example, the genes for AOX1c (four elements), cytochrome P450 (five elements), L: -asparaginase (five elements), and PCF8 (two elements). Four elements, AnacA1-A4, have both the AOX1c and P450 genes. One element, AnacB14, involves a gene similar to mudrA of maize MuDR. Database analyses revealed that the loci of 26 of the 27 Anaconda elements in the subspecies japonica are the same as those in the subspecies indica. This suggests that these elements were incorporated before the divergence of these two subspecies.

Amino Acid Sequence↗
PubMed1984

The DNA sequence and genetic organization of a Neurospora mitochondrial plasmid suggest a relationship to introns and mobile elements.

We have determined the complete 3581 bp sequence of the mitochondrial plasmid from Neurospora crassa strain Mauriceville-1c. The plasmid contains a long open reading frame that is expressed in its major transcript and could encode a hydrophilic protein of 710 amino acids. Two characteristics of the plasmid--codon usage and the presence of conserved sequence elements--suggest that it is related to Group I mtDNA introns. The major transcripts of the plasmid are approximately full-length, colinear RNAs that have heterogenous 5' ends and a single major 3' end. The major 5' and 3' ends are adjacent and slightly overlapping. The Mauriceville plasmid may belong to a class of genetic elements that were or are the progenitors of mtDNA introns.

Base Sequence↗
PubMed1992

The 28S ribosomal RNA-encoding gene of Hymenoptera: inserted sequences in the retrotransposon-rich regions.

The genomes of two parasitoid wasps, Diadromus pulchellus and Eupelmus vuilleti, and the honey bee, Apis mellifera, contain few interspersed repeated sequences corresponding to transposons (Tn). This suggests that the genomic organisation of Hymenoptera could be due to the elimination of deleterious Tn in haploid males. We have used restriction-fragment length polymorphism analysis to show that nondeleterious Tn are present in the DNA (rDNA) encoding ribosomal RNA of twelve species of Hymenoptera. Sequence analysis of the 28S rDNA type-I and type-II insertion-rich regions of 80 species showed that this region is very highly conserved (95.8%). A consensus sequence and restriction map of the rDNA region were established. These sequence data were used to develop a strategy for detecting inserted elements in the rDNA fragments containing type-I or type-II insertion sites, and this strategy was used to screen twelve hymenopteran species and four non-Hymenoptera control species. The rDNA fragments from the Hymenoptera and control species contained inserted sequences in the area where type-I and type-II elements are inserted in the 28S rDNA retrotransposon-rich region of Diptera and Lepidoptera. The hymenopteran genomes therefore appear to contain repeated elements, the mobility and nature of which remain to be determined.

Animals↗
PubMed2001

Evolutionary history of the impala transposon in Fusarium oxysporum.

Impala is an active DNA transposon family that was first identified in a strain of Fusarium oxysporum pathogenic to melon. The 10 copies present in this strain define three subfamilies that differ by about 20% at the nucleotide level. This high level of polymorphism suggests the existence of an ancestral polymorphism associated with vertical transmission and/or the introduction of some subfamilies by horizontal transfer from another species. To gain insights into the molecular evolution of this family, impala distribution was investigated in strains with various host specificities by Southern blot, PCR, and sequencing. Detection of impala elements in most of the F. oxysporum strains tested indicates that impala is an ancient component of the F. oxysporum genome. Subfamily-specific amplifications and sequence and phylogenetic analyses revealed five subfamilies, several of which can be found within the same genome. This supports the hypothesis of an ancestral polymorphism followed by vertical transmission and independent evolution in the host-specific forms. Highly similar elements showing unique features (internal deletions, high rates of CG-to-TA transitions) or being present at the same genomic location were identified in several strains with different host specificities, raising questions about the phylogenetic relationships of these strains. A phylogenetic analysis performed by sequencing a portion of the EF1alpha gene showed in most cases a correlation between the presence of a particular element and a close genetic relationship. All of these data provide important information on the evolutionary origin of this element and reveal its potential as a valuable tool for tracing populations.

Base Sequence↗
PubMed1993

Sequence relationship of retrotransposable elements R1 and R2 within and between divergent insect species.

R1 and R2 are retrotransposable elements that integrate at specific sites in the 28S ribosomal RNA (rRNA) genes of Bombyx mori and Drosophila melanogaster. We have previously shown that most insect species contain insertions in their 28S genes at the R1 and/or R2 site. We have sequenced the 3' half of R1 and R2 elements from three additional insect species: the fungus gnat, Sciara coprophila (Diptera); the Japanese beetle, Popillia japonica (Colleoptera); and the parasitic wasp, Nasonia vitripennis (Hymenoptera). The elements were obtained by screening lambda phage genomic clones containing rDNA units and by a polymerase chain reaction approach using degenerate primers to conserved sequences in the reverse-transcriptase domain, in combination with a second primer to the 28S gene 3' of the insertion site. Comparisons of the sequences of R1 and R2 from four insect orders suggest that the organization of their open-reading frames has been conserved and is therefore likely to be similar throughout insects. This sequence analysis also indicates that, except for 5' truncations generated during the retrotransposition process itself, most elements have not accumulated mutations that would make them inactive. Popillia japonica and N. vitripennis differed from previously described species, in that (a) P. japonica contained multiple families of R2 and (b) N. vitripennis contained multiple families of R1. Nucleotide sequence identity between these different families is low. Amino acid sequence identity of their open-reading frames averaged only 41% for the R2 families of P. japonica and 35% for the R1 families of N. vitripennis. The presence of multiple highly divergent families of elements within a species suggests either that each insertion family is able to maintain its copy number without eliminating the other families in its competition for a limited number of 28S genes or that there has been extensive horizontal transfer of R1 and R2 elements between insect species.

Amino Acid Sequence↗
PubMed1987

The R46 site-specific recombination system is a homologue of the Tn3 and gamma delta (Tn1000) cointegrate resolution system.

The nucleotide sequence of the R46 site-specific recombination system has been determined. The organization of the recombination gene (perR46) and the site at which it acts (per site), together with the extensive sequence homology displayed with the tnpR genes and res sites of the transposons Tn3 and gamma delta (Tn1000), suggests that they have been derived from a Tn3-like element. These site-specific recombination functions of R46 play a role in plasmid maintenance.

Base Sequence↗
PubMed1998

IS990, a new species-specific insertion-sequence-related element of the Mycobacterium tuberculosis complex.

The structure and distribution of 1S990, a new Mycobacterium tuberculosis DNA sequence with homology to characterized insertion sequences (ISs), were investigated. IS990 was related to IS elements of the IS3 family and was present as a single copy in all 21 investigated M. tuberculosis strains, two Mycobacterium bovis strains and two M. bovis BCG strains. The sequence appears to be specific for the M. tuberculosis complex. The element carries two frameshift mutations and appears to be defective.

Amino Acid Sequence↗