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At least 865 records · Page 48Linked to original sources
PubMed2002

Transposon Tn1721 distribution among strains of Xylella fastidiosa.

Transposons are mobile genetic elements found within the genomes of various organisms including bacteria, fungi, plants and animals. Fragments of the transposon Tn1721 were found included in the genome of Xylella fastidiosa strain 9a5c. Regions from such fragments were PCR-amplified using specially designed primers (TNP(1) and TNP(2)). In order to detect insertions of the Tn1721 element, both primers were used and one of them included a region of the transposon (TNP(1)) and the other one had the right repeat and part of the bacterial chromosome (TNP(2)). The PCR products obtained from strain 9a5c were used as a pattern for fragment size comparisons when DNA samples from other X. fastidiosa strains were used as template for the PCR assays. Differences were observed concerning the PCR products of such amplifications when some X. fastidiosa strains isolated from grapevine and plum were used. For the citrus-derived strains only the strains U187d and GP920b produced fragments with different sizes or weak band intensity. Such variations in the X. fastidiosa genome related to disrupted Tn1721 copies are probably due to the possibility of such a transposon element being still able to duplicate even after deletion events might have taken place and also because the bacterial strains in which the main differences were detected are derived from different host plants cultivated under different climate conditions from the one used as reference.

Base Sequence↗
PubMed1990

Localization of sequences required in cis for yeast Ty1 element transposition near the long terminal repeats: analysis of mini-Ty1 elements.

In order to identify and characterize sequences within Ty1 elements which are required in cis for transposition, a series of mini-Ty1 plasmids were constructed and tested for transposition. Mini-Ty1s are deletion mutants of the Ty1-H3 element; Ty1 gene products required for transposition are supplied in trans from a helper Ty1 which has intact open reading frames but lacks a 3' long terminal repeat (LTR) and therefore cannot transpose itself. Up to 5 kilobase pairs of internal sequences of the 6-kilobase-pair-long Ty1 element can be deleted without a significant effect on transposition. The smallest mini-Ty1 element capable of transposition contains the 3' LTR and the transcribed portion of the 5' LTR, 285 base pairs (bp) of internal sequence 3' to the 5' LTR, and 23 bp of internal sequence 5' to the 3' LTR. We conclude that Ty1-encoded proteins can act in trans and that cis-acting sequences in Ty1-H3 are all within or near the LTRs. Further deletion of the 285-bp internal sequence adjacent to the 5' LTR significantly reduced transposition frequency, and the mini-Ty1 RNA produced failed to be packaged into the viruslike particles efficiently. Surprisingly, several nonhomologous cellular mRNAs were also associated with viruslike particles.

Base Sequence↗
PubMed1994

Characterization of transposon Tn1528, which confers amikacin resistance by synthesis of aminoglycoside 3'-O-phosphotransferase type VI.

Providencia stuartii BM2667, which was isolated from an abdominal abscess, was resistant to amikacin by synthesis of aminoglycoside 3'-O-phosphotransferase type VI. The corresponding gene, aph(3')-VIa, was carried by a 30-kb self-transferable plasmid of incompatibility group IncN. The resistance gene was cloned into pUC18, and the recombinant plasmid, pAT246, was transformed into Escherichia coli DH1 (recA) harboring pOX38Gm. The resulting clones were mixed with E. coli HB101 (recA), and transconjugants were used to transfer pAT246 by plasmid conduction to E. coli K802N (rec+). Analysis of plasmid DNAs from the transconjugants of K802N by agarose gel electrophoresis and Southern hybridization indicated the presence of a transposon, designated Tn1528, in various sites of pOX38Gm. This 5.2-kb composite element consisted of aph(3')-VIa flanked by two direct copies of IS15-delta and transposed at a frequency of 4 x 10(-5). It therefore appears that IS15-delta, an insertion sequence widely spread in gram-negative bacteria, is likely responsible for dissemination to members of the family Enterobacteriaceae of aph(3')-VIa, a gene previously confined to Acinetobacter spp.

Amikacin↗
PubMed1994

Nucleotide sequence and analysis of an insertion sequence from Bacillus thuringiensis related to IS150.

A 5.8-kb DNA fragment encoding the cryIC gene from Bacillus thuringiensis (Bt) subsp. aizawai HD229 was subcloned into the pMex7 vector for expression in Escherichia coli. In addition to the 135-kDa CryIC delta-endotoxin, this DNA fragment also encoded a 30-kDa polypeptide whose open reading frame (orfX) was located less than 200 bp upstream of cryIC. Nucleotide sequencing showed that orfX was truncated at the 5' end, and full sequence was obtained from a second overlapping clone. Sequence analysis showed that orfX could encode a polypeptide closely related to the putative transposase from IS150. OrfX was flanked by a 17-bp imperfect inverted repeat, defining the length of the element as 998 bp. Southern blot analysis revealed that the novel insertion sequence was present in a single copy and located in an identical position immediately upstream of cryIC in plasmid DNA from both Bt subsp. aizawai and entomocidus.

Amino Acid Sequence↗
PubMed1986

Repeated sequences with unusual properties from the divergent region of Crithidia oncopelti maxicircle kinetoplast DNA.

The occurrence of bacterial promoter-like sequences was shown in the divergent region of Crithidia oncopelti maxicircular kinetoplast DNA. A promoter-cloning vector based on the neomycin phosphotransferase II (NPT II) gene was used to localize promoters in three homologous blocks of repeated sequences. The elements found displayed greater promoter strength in Escherichia coli than the normal promoter of the NPT II gene. Sequences of three promoter-containing inserts from different blocks were determined and typical prokaryotic promoter sequences were localized.

Animals↗
PubMed1999

Epigenetic interactions among three dTph1 transposons in two homologous chromosomes activate a new excision-repair mechanism in petunia.

Unstable anthocyanin3 (an3) alleles of petunia with insertions of the Activator/Dissociation-like transposon dTph1 fall into two classes that differ in their genetic behavior. Excision of the (single) dTph1 insertion from class 1 an3 alleles results in the formation of a footprint, similar to the "classical" mechanism observed for excisions of maize and snapdragon transposons. By contrast, dTph1 excision and gap repair in class 2 an3 alleles occurs via a newly discovered mechanism that does not generate a footprint at the empty donor site. This novel mechanism depends on the presence of two additional dTph1 elements: one located in cis, 30 bp upstream of the an3 translation start in the same an3 allele, and a homologous copy, which is located in trans in the homologous an3 allele. Absence of the latter dTph1 element causes a heritable suppression of dTph1 excision-repair from the homologous an3 allele by the novel mechanism, which to some extent resembles paramutation. Thus, an epigenetic interaction among three dTph1 copies activates a novel recombination mechanism that eliminates a transposon insertion.

Alleles↗
PubMed1997

Mutations in the hrp48 gene, which encodes a Drosophila heterogeneous nuclear ribonucleoprotein particle protein, cause lethality and developmental defects and affect P-element third-intron splicing in vivo.

The Drosophila melanogaster hnRNP protein, hrp48, is an abundant heterogeneous nuclear RNA-associated protein. Previous biochemical studies have implicated hrp48 as a component of a ribonucleoprotein complex involved in the regulation of the tissue-specific alternative splicing of the P-element third intron (IVS3). We have taken a genetic approach to analyzing the role of hrp48. Mutations in the hrp48 gene were identified and characterized. hrp48 is an essential gene. Hypomorphic mutations which reduce the level of hrp48 protein display developmental defects, including reduced numbers of ommatidia in the eye and morphological bristle abnormalities. Using a P-element third-intron reporter transgene, we found that reduced levels of hrp48 partially relieve IVS3 splicing inhibition in somatic cells. This is the first direct evidence that hrp48 plays a functional role in IVS3 splicing inhibition.

Animals↗
PubMed1995

Enterococcus faecalis plasmid pAD1 replication and maintenance.

A determinant has been identified which is required for the stable inheritance of a replicon isolated from the pheromone-responsive E. faecalis plasmid pAD1. This determinant, called par, is encoded on a DNA fragment no larger than 457 bp and directs the production of two small RNAs of approximately 250 (RNAI) and 145 (RNAII) nucleotides. Mutations affecting par RNA production also affected plasmid stability, indicating that these RNAs play a central role in par function. Putative transcription start sites were identified within par by DNA sequence analysis, but the sizes of the observed RNAs and the effects of transposon inserts on RNA production are not entirely consistent with predictions based on the hypothetical RNAs produced from these start sites. The absence of clearly functional open reading frames and the presence of various sequence repeat elements within par suggest that these RNAs may not be translated but may perform some structural role in the partition apparatus. The isolated par determinant was capable of producing both RNAs and stabilizing a heterologous vector, indicating that no other pAD1-encoded determinants are required for par function.

Base Sequence↗
PubMed1995

Improvement of S-adenosylmethionine production by integration of the ethionine-resistance gene into chromosomes of the yeast Saccharomyces cerevisiae.

An ethionine-resistance gene cloned from Saccharomyces cerevisiae DKD-5D-H was able to enhance S-adenosyl-L-methionine (AdoMet) accumulation when it was introduced into the yeast cells on multi-copy plasmid YEp13. In order to increase the AdoMet accumulation, the gene was integrated into the yeast chromosome by using a yeast transposon Ty element. When the YEp plasmid was used for the integration, the ethionine-resistance gene was efficiently inserted into the yeast chromosomes with a substantial increase in AdoMet productivity (about twofold) in comparison with that by the yeast cells carrying the gene on an extrachromosomal multi-copy plasmid.

Biotechnology↗
PubMed1989

Isolation and characterization of ribosomal DNA variants from Sciara coprophila.

The ribosomal RNA multigene family in the fungus fly Sciara coprophila contains a total of only 65 to 70 repeat units. We explored the types and frequencies of variant repeats in this small multigene family by characterizing different cloned rDNA variants from Sciara. Although we did not observe any intergenic spacer length variants in Sciara, we found a variant due to the insertion of a putative mobile element (lambda Bc11), and variants containing ribosomal insertion elements. By DNA sequence analysis of rDNA/non-rDNA junctions, there are three distinct types of ribosomal insertion elements found in Sciara rDNA: two correspond to the R1 and R2 insertion elements found in other dipterans (clones lambda Bc5 and pBc1L1, respectively), and one is a novel class of ribosomal insertion elements (R3, exemplified by clone pBc6D6) which so far is unique to Sciara. Together, the several different rDNA variants make up from 12 to 20% of the rDNA in Sciara. These results are discussed in the context of evolution of the ribosomal RNA multigene family.

Animals↗
PubMed2004

Comparative analysis of the complete cag pathogenicity island sequence in four Helicobacter pylori isolates.

The cytotoxin-associated gene (cag) pathogenicity island (PAI) is important for the virulence of Helicobacter pylori. In this study, we have compared the complete nucleotide sequence of the cag PAI in four clinical isolates. These isolates were selected from patients matched for age and sex from the same geographical region. The patients suffered from either gastric cancer (Ca52 and Ca73) or duodenal ulcer (Du23:2 and Du52:2). All four strains induced an interleukin (IL)-8 response in AGS cells and translocated CagA into host cells where the protein was tyrosine phosphorylated, and thus harboured a functional type IV secretion system encoded by the cag PAI. The cagA gene contains a variable region close to its 3' end. Different compositions of this region has been proposed to exert various degrees of morphological changes in cultured gastric epithelial cells, and there are indications that the structure of the repetitive region is connected to the severity of disease. One of the studied strains (Du23:2) possessed five Western-type repeat regions while the other three strains harboured one Western-type repeat. Strain Du23:2 also contained a major rearrangement or large insertion/duplication in the intergenic region between HP0546 and HP0547 (cagA). Sequence similar to that of genes HP0510 and HP0509 was found in the 5' end of this region. The 3' end was similar to the corresponding region of strain ATCC 43504, including a mini IS605 element and a duplication of the 3' end of the cag PAI. Finally, a novel gene was identified in the cag PAI in three of the sequenced strains at the position of HP0521. This gene, HP0521B, is present in approximately half of Swedish H. pylori isolates.

Antigens, Bacterial↗
PubMed2003

Spontaneous muscular dystrophy caused by a retrotransposal insertion in the mouse laminin alpha2 chain gene.

We identified a novel spontaneous mouse model of human congenital muscular dystrophy with laminin alpha2 chain deficiency, named dy(Pas)/dy(Pas). Homozygous animals rapidly developed a progressive muscular dystrophy leading to premature death. Immunohistological and biochemical analyses demonstrated the absence of laminin alpha2 chain expression in skeletal muscle. Analysis of the laminin alpha2 chain cDNA showed the insertion of the long terminal repeat of an intracisternal A-particle gene. In addition, a 6.1 kb insertion composed of retrotransposon elements was identified in the Lama2 sequence. The dy(Pas)/dy(Pas) mouse is thus the first spontaneous mutant with a complete laminin alpha2 chain deficiency in which the mutation has been identified.

Animals↗
PubMed1981

Terminal direct repeats in a retrovirus-like repeated mouse gene family.

The mouse genome contains multiple copies of a dispersed gene family known individually as VL30 genes which are thought to be associated with retroviruses. The copies consist of closely related 5.2-kilobase DNA sequences flanked by unrelated cellular DNA, and although no sequence homology has been found between the genes and the exogenous or endogenous retroviruses so far tested, the 30S RNA transcripts expressed by the genes are efficiently packaged into virions, recovered from infected cells and transmitted to other cells by pseudo-type infection. Stimulated by recent reports of the similarity between retroviruses and transposons (from which retroviruses may have evolved), and in particular by the recognition that both types of genetic elements are characterized by a large terminal repeat (LTR), we set out to determine whether the VL30 genes are also distinguished by this property. Using cloned DNAs from a mouse gene library and heteroduplex analysis, we have now found that the VL30 genes do indeed carry terminal direct repeats 400 base pairs long.

Animals↗
PubMed1996

Organizational characteristics and information content of an archaeal genome: 156 kb of sequence from Sulfolobus solfataricus P2.

We have initiated a project to sequence the 3 Mbp genome of the thermoacidophilic archaebacterium Sulfolobus solfataricus P2. Cosmids were selected from a provisional set of minimally overlapping clones, subcloned in pUC18, and sequenced using a hybrid (random plus directed) strategy to give two blocks of contiguous unique sequence, respectively, 100,389 and 56,105 bp. These two contigs contain a total of 163 open reading frames (ORFs) in 26-29 putative operons; 56 ORFs could be identified with reasonable certainty. Clusters of ORFs potentially encode proteins of glycogen biosynthesis, oxidative decarboxylation of pyruvate, ATP-dependent transport across membranes, isoprenoid biosynthesis, protein synthesis, and ribosomes. Putative promoters occur upstream of most ORFs. Thirty per cent of the predicted strong and medium-strength promoters can initiate transcription at the start codon or within 10 nucleotides upstream, indicating a process of initial mRNA-ribosome contact unlike that of most eubacterial genes. A novel termination motif is proposed to account for 15 additional terminations. The two contigs differ in densities of ORFs, insertion elements and repeated sequences; together they contain two copies of the previously reported insertion sequence ISC 1217, five additional IS elements representing four novel types, four classes of long non-IS repeated sequences, and numerous short, perfect repeats.

Chromosomes, Bacterial↗
PubMed1985

Transposable element IS1 intrinsically generates target duplications of variable length.

Target duplication during transposition is one of the characteristics of mobile genetic elements. IS1, a resident insertion element of Escherichia coli K-12, was known to generate a 9-base-pair target duplication, while an IS1 variant, characterized by a nucleotide substitution in one of its terminal inverted repeats, was reported to duplicate 8 base pairs of its target during cointegration. We have constructed a series of transposons flanked by copies of either the normal or the variant IS1. The analysis of their transposition products revealed that transposons with normal termini as well as those with variant termini can intrinsically generate either 9- or 8-base-pair target duplications. We also observed that a normal IS1 from the host chromosome generated an 8-base-pair repeat. The possible relevance of the observation for the understanding of transposition processes and models to explain the variable length of target duplications are discussed.

Base Sequence↗
PubMed1990

Ty virus-like particles in the Saccharomyces cerevisiae strain NCYC74.

Electron microscopic analysis of thin sections of Saccharomyces cerevisiae NCYC74 has revealed the presence of many clumped cytoplasmic particles that morphologically resemble Ty element virus-like particles (VLPs). Accumulation of Ty VLPs has only previously been observed in S. cerevisiae strains that over-express a cloned Ty element. The particles in NCYC74 co-purify with Ty RNA, Ty-specific antigens and a reverse transcriptase activity. Furthermore, they appear to be recognized by antibodies to Ty VLPs during indirect immunofluorescence experiments. These observations provide compelling evidence that the cytoplasmic particle in NCYC74 are indeed Ty VLPs.

Blotting, Southern↗
PubMed1981

Distribution of IS5 in bacteria.

Four different strains of Escherichia coli and several other bacteria were examined by Southern analysis for the presence of the insertion element IS5 and IS5-like sequences. Variations in the copy number, degree of homology and restriction pattern of the IS5-like sequence were found among the different organisms. The number and distribution of IS5 sequences do not appear to correlate with the evolutionary relationship of the bacteria in which they occur.

Bacillus subtilis↗