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At least 1,405 records · Page 78Linked to original sources
PubMed1999

Genetic structure and transcriptional analysis of a mobilizable, antibiotic resistance transposon from Bacteroides.

Tn4555 is a 12.1-kb Bacteroides antibiotic resistance transposon representative of a novel class of transmissible genetic elements that can be transferred by resident conjugative tetracycline resistance transposons (Tc(r)-elements) but are not capable of self-transfer. Previously it was shown that Tn4555 transposes by a site-specific recombination mechanism that utilizes a circular intermediate. This circular form is induced by tetracycline and it also is the substrate for conjugation. To better understand the mechanism of transposition, the entire nucleotide sequence of Tn4555 was determined and a set of genes potentially involved in transposition was identified. The transposon was 12,105 bp including a variable 6-bp coupling sequence associated with one of the transposon termini. The element had a 44.3% G + C composition and nine potential protein coding regions were observed, eight of which were encoded on the forward strand. Two putative transposition genes were found. The int gene product had significant C-terminal homology to the lambda family of integrases and the xis gene product was similar to several excisionase proteins encoded by both plasmids and conjugative transposons. The mobA mobilization gene and cfxA beta-lactamase gene of Tn4555 had been previously identified, and the remaining five open reading frames had no significant matches with sequences in the available databases. Northern hybridization analysis revealed that all Tn4555 genes except for orf-9 were expressed and two sets of genes, tnpA, int and xis, orf-5, orf-6 were organized in operons. None of the genes seemed to be induced significantly by the addition of tetracycline to cultures. Although a small 0.4-kb xis-specific transcript appeared in tetracycline-treated cultures it was not clear if this was due to an induction or if it was a specific degradation product.

Amino Acid Sequence↗
PubMed1993

The majority of simian immunodeficiency virus/mne circle junctions result from ligation of unintegrated viral DNA ends that are aberrant for integration.

SIV/Mne circle junctions were amplified by the polymerase chain reaction (PCR) and cloned in a bacterial plasmid. Sequence analysis of clones isolated from 11 independent PCRs reveals that the start site for plus DNA synthesis is 5' ACTG. . ., and thus an asymmetric cleavage must occur during viral integration. In addition, most of the sequences found resulted from the ligation of aberrant proviral DNA ends that were apparently generated by priming errors, primer removal errors, or integrase processing errors. The results suggest that in this virus, as in Moloney murine leukemia virus, two good ends may be required for efficient integration.

Base Sequence↗
PubMed1997

Characterization of the lysogeny DNA module from the temperate Streptococcus thermophilus bacteriophage phi Sfi21.

Phage phi Sfi21, the only temperate Streptococcus thermophilus phage from our phage collection, showed extensive DNA homology with virulent phages from lytic group I. Southern blot hybridizations demonstrated that the phi Sfi21-specific DNA was clustered in an approximately 6.6-kb-long region, the putative lysogeny module. Sequence analysis and database research identified an integrase within this module; orf 203 with homology to an anonymous orf 258 from the temperate lactococcal phage BK5-T; orf 127 and orf 122 with weak homology to the N- and C-terminal parts, respectively, of the cl-like repressor from lactococcal phages Tuc2009 and BK5-T; orf 75 with homology to a repressor protein from lambdoid phage 434 and an anti-repressor ant with homology to phage P1. The molecular arrangement of the predicted orfs in phage phi Sfi21 was very similar to that of the lactococcal phage BK5-T. The transition from phi Sfi21-specific DNA into DNA shared with virulent phages was abrupt and flanked at one side by notable DNA repeats. Sequence analysis identified a holin protein to the left of the lysogeny module. A site-specific deletion of 2.4 kb, which reproducibly transformed phi Sfi21 into a lytic phage, was localized in the lysogeny module. It was flanked at both sides by conspicuous DNA repeats. One repeat region reflected the DNA around the attP site, while the other reflected the putative genetic switch region between repressor and anti-repressor genes. S. thermophilus host Sfi1 transformed with a plasmid containing int and orf 203 showed resistance to superinfection by heterologous phages, but not by the homologous phi Sfi21. Part of the int gene could be deleted without loss of this activity, while a deletion in orf 203 resulted in loss of the phage resistance. We speculate on the possibility of a bipartite immunity system for the control of lysogeny in phi Sfi21.

Amino Acid Sequence↗
PubMed1998

The site-specific recombination system of the Lactobacillus species bacteriophage A2 integrates in gram-positive and gram-negative bacteria.

The region of the bacteriophage A2 genome involved in site-specific recombination with the DNA of Lactobacillus spp. has been identified. Two orfs, transcribed from the same strand, have been found immediately upstream of the phage attachment site (attP). The orf adjacent to attP predicts a 385-amino-acid protein that presents significant similarity with site-specific recombinases of the integrase family. The other orf encodes a basic polypeptide of 76 amino acid residues. The junctions of the prophage with the genomes of its hosts have been determined, allowing the identification of the host attachment site (attB), which has a common 19-nucleotide core region with attP. The attB site is located at the 3' end of the transfer RNALeu gene (anticodon CAA). Nonreplicative plasmids containing the A2-specific recombination cassette integrate into different lactobacilli but also into unrelated Gram-positive bacteria such as Lactococcus lactis and even into Escherichia coli. In Lc. lactis, integration occurs in a previously unknown intergenic region, whereas in E. coli, it maps within the rrnD operon, 5' of rrsD gene. Comparison of the integration sites in the different hosts indicates that some flexibility is permitted in the attB sequence, since Lc. lactis and E. coli only share 13 and 11 nucleotides, respectively, with the 19-nucleotide core sequence of the lactobacilli.

Amino Acid Sequence↗
PubMed2002

Complete genomic sequence of bacteriophage ul36: demonstration of phage heterogeneity within the P335 quasi-species of lactococcal phages.

The complete genomic sequence of the Lactococcus lactis virulent phage ul36 belonging to P335 lactococcal phage species was determined and analyzed. The genomic sequence of this lactococcal phage contained 36,798 bp with an overall G+C content of 35.8 mol %. Fifty-nine open reading frames (ORFs) of more than 40 codons were found. N-terminal sequencing of phage structural proteins as well as bioinformatic analysis led to the attribution of a function to 24 ORFs (41%). A lysogeny module was found within the genome of this virulent phage. The putative integrase gene seems to be the product of a horizontal transfer because it is more closely related to Streptococcus pyogenes phages than it is to L. lactis phages. Comparative genome analysis with six complete genomes of temperate P335-like phages confirmed the heterogeneity among phages of P335 species. A dUTPase gene is the only conserved gene among all P335 phages analyzed as well as the phage BK5-T. A genetic relationship between P335 phages and the phage-type of the BK5-T species was established. Thus, we proposed that phage BK5-T be included within the P335 species and thereby reducing the number of lactococcal phage species to 11.

Bacteriophages↗
PubMed1992

Sequence analysis of WIS-2-1A, a retrotransposon-like element from wheat.

WIS-2-1A, a 8624 bp insertion in the Glu-1A-2 locus of chromosome 1A of wheat, consists of two 1755 bp long terminal repeats enclosing a 5114 bp internal region. No long open reading frames could be found, but inspection of the predicted amino acid sequence showed regions with homology to retrotransposon structures, including a methionine tRNA initiator binding site, a nucleotide binding domain, a protease, an integrase and a polymerase. DNA replication errors have resulted in frame-shifts in the protein coding region, suggesting that retrotransposition of WIS-2-1A, if it occurs, must be mediated by trans-acting factors.

Amino Acid Sequence↗
PubMed1994

Structural organization of str 246C and str 246N, plant defense-related genes from Nicotiana tabacum.

We have previously identified a cDNA clone, pNt246, whose corresponding transcripts accumulate in leaves in response to inoculation by compatible and incompatible isolates of the phytopathogenic bacterium Pseudomonas solanacearum [19]. We now describe the nucleotide sequence of a genomic clone, str 246C, corresponding to this cDNA species, and of a related genomic clone, str 246N, which appears to be a pseudogene with a 5'-end deletion. The nucleotide sequence of the str 246C gene was found to be identical to that of the parA gene, previously shown to be regulated by auxin [28, 29]. Upstream of the str 246N gene, sequences homologous to a Bam HI repetitive element described in Vicia faba [15] are present within an ORF showing significant homologies to an integrase-encoding gene of several retroviruses. This observation indicates that this highly repetitive DNA originates from sequences present in transposable mobile elements.

Amino Acid Sequence↗
PubMed1992

Lambdoid phages as elements of bacterial genomes (integrase/phage21/Escherichia coli K-12/icd gene).

The lambdoid phages are a group of related temperate bacteriophages that lysogenize by site-specific recombination with the bacterial chromosome. Various members of the group have different specific chromosomal insertion sites, despite the fact that the enzymes catalyzing the insertion (integrases) appear to be all descended from a common ancestor. Insertion sites are not located randomly on the E. coli chromosome but are restricted to one segment of the map; also, most prophages are oriented in the same direction along the chromosome. Lambdoid phage 21 inserts within the isocitrate dehydrogenase gene and introduces an alternative 165 bp 3' end for that gene. A defective element (e14) inserts at the same position. We suggest that this mode of insertion arose from insertion of an ancestral phage to the right of icd which then picked up part of the icd gene by abnormal excision and speculate that, at an earlier time, phages may have arrived at their present locations by a process of chromosomal walking.

Bacterial Proteins↗
PubMed1990

Occurrence of a copia-like transposable element in one of the introns of the potato starch phosphorylase gene.

The gene coding for starch phosphorylase (EC 2.4.1.1) was isolated from a potato genomic library constructed in lambda EMBL3. It is an unusually long plant gene (16.4 kb) which encodes a preprotein of 966 amino acids. The phosphorylase coding sequence is interrupted by 14 introns whose positions do not match those of the introns in the human glycogen phosphorylase gene. A 78 amino acid central peptide unique to plant plastidial phosphorylases is hypothesized to have arisen through the mis-splicing of an intron-exon junction site in an ancestral gene. The fifth intron of the phosphorylase is very large (approximately 7 kb) and contains a copia-like transposable element inserted in the opposite orientation to that of the phosphorylase gene. This element has been named Tst1; it is bordered on the 5' and 3' sides by long terminal repeats of 285 and 283 bp respectively, which define an internal domain of 4492 bp. Tst1 contains 4 open reading frames (ORFs) that encode protein domains for a reverse transcriptase, an integrase, an RNA-binding site and a protease. Transcription of the phosphorylase gene appears to proceed unimpaired through the copia element.

Amino Acid Sequence↗
PubMed1991

Site-specific recombination in Escherichia coli between the att sites of plasmid pSE211 from Saccharopolyspora erythraea.

pSE211 from Saccharopolyspora erythraea integrates site-specifically into the chromosome through conservative recombination between attP and attB, the plasmid and chromosomal attachment sites. Integration depends on the presence of int, an open reading frame (ORF) that lies adjacent to attP and encodes the putative integrase. Immediately upstream of int lies xis (formerly called orf2) which encodes a basic protein that is thought to exhibit DNA binding. xis and int were cloned in various combinations in pUC18 and expressed constitutively in Escherichia coli from the lac promoter. attP and attB were cloned in Streptomyces or E. coli plasmids containing kanamycin resistance (KmR) or chloramphenicol resistance (CmR) markers. Stable KmR CmR cointegrates formed by attP x attB or attP x attP recombination (integration) were obtained in E. coli hosts that expressed int. Co-integrates were not found in hosts expressing int + xis. Excision (intraplasmid att site recombination) was examined by constructing plasmids carrying attL and attR or two attP sites separating CmR from KmR and by following segregation of the markers in various hosts. Both attL x attR and attP x attP excision depended on both xis and int in E. coli. pSE211 att site integration and excision were not affected by a deletion in himA, the gene encoding a subunit of integration host factor.

Actinomycetales↗
PubMed1993

Transcriptional analysis of the Chlamydia trachomatis plasmid pCT identifies temporally regulated transcripts, anti-sense RNA and sigma 70-selected promoters.

We analysed transcription of the DNA region immediately downstream of the origin of replication in the chlamydial plasmid pCT. This region comprises two convergent open reading frames (ORF7, ORF8), encoding putative polypeptides that are homologous to each other and with C-terminal domains typical of the phage integrase family of proteins. Northern blot and RNA 5' end mapping analyses indicated that both ORFs were transcribed in the late phase of the chlamydial replicative cycle. RNA mapping showed the presence of a transcript starting 31 nucleotides (nt) before the ATG start codon of ORF7, and two temporally regulated transcripts starting 59 and 89 nt upstream of the ATG start codon of ORF8. Two abundant RNA species of 225 and 415 nt were also identified as overlapping anti-sense transcripts (AS-RNAs), complementary to the 3' end of ORF8 mRNA, with identical 5' ends but different 3' ends. In vitro and in vivo experiments in Escherichia coli showed that the sigma 70-RNA polymerase complex was capable of initiating RNA synthesis at the same sites as observed in Chlamydia trachomatis for ORF7 and AS-RNA transcripts, but was not able to transcribe ORF8. In accord with this, sequences at -10 and -35 nt upstream of the RNA 5' ends resemble sigma 70 consensus promoters in the case of ORF7 and AS, but not in the case of the two ORF8 transcripts. Therefore, transcription of ORF7 and ORF8 is controlled by different types of promoters.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1994

Position and direction of strand exchange in bacteriophage HK022 integration.

The positions of the endonucleolytic cleavages promoted by the integrase protein (Int) of coliphage HK022 within its attB site were determined. The protein catalyses a staggered cut, which defines an overlap sequence of 7 bp within the core site. The overlap region is at the center of symmetry of a palindromic sequence which appears in all four putative att core binding sites for Int. We confirm that the order of strand exchange is similar to that in phage lambda.

Attachment Sites, Microbiological↗
PubMed1984

Cloning of the integration and attachment regions of bacteriophage P4.

The integration and attachment regions of bacteriophage P4 have been cloned into a multicopy plasmid. This plasmid can integrate into the E. coli chromosome at the same location as the parent phage. Integration increases the stability of the plasmid and allows it to be retained even under conditions in which a non-integrated plasmid would be lost. None of the genes needed for P4 lytic growth is required for integration. The P4 integration and attachment regions have been cloned on separate plasmids. A plasmid that carries the attachment site can integrate into the chromosome only if another plasmid that carries the P4 integration functions is present. A plasmid that carries only this trans-acting integration function cannot integrate. Using deletion mutants of the plasmid, the maximum size of the region needed for integration has been determined to be 1.6 kb, of which no more than 1.2 kb codes for the integrase protein. A nonsense mutant defective in integration has been isolated by using a rapid screening procedure that identifies unstable plasmids.

Base Sequence↗
PubMed1994

Characterization of the genes and attachment sites for site-specific integration of plasmid pSE101 in Saccharopolyspora erythraea and Streptomyces lividans.

The 11.3 kb plasmid pSE101 integrates into the chromosome of Saccharopolyspora erythraea at a specific attB site and into the chromosome of Streptomyces lividans at many sites. Multisite integration in S. lividans was also observed when a 1.9 kb segment of pSE101 containing attP and adjacent plasmid sequence was used to transform a pSE101- S. lividans host. Nucleotide sequencing of this segment revealed the presence of a complete open reading frame (ORF) designated int, encoding a putative polypeptide of 448 amino acids that shows similarities to site-specific recombinases of the integrase family. Sequencing of the 1.3 kb segment upstream of int revealed the presence of three additional ORFs: the one most distal to int encodes a putative 76 amino acid basic polypeptide analogous to the Xis proteins of a number of bacteriophages. Nucleotide sequencing of attP, and the attB, attL and attR sites from Sac. erythraea revealed a 46 bp sequence common to all sites with no duplications of chromosomal sequences in the integrated state. A putative structural gene for a tRNA(Thr) was found to overlap the 46 bp common sequence at attB. Sequencing of four pSE101 integration sites (attB') and corresponding attL' and attR' sites in S. lividans showed that the 46 bp sequence was present at each attR' site, whereas only the first three bases, CTT, were retained at each attL' and attB' site. A feature common to the four attB' sites and to attB is a highly conserved 21 bp segment with inverted repeats flanking the CTT sequence.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1995

Skippy, a retrotransposon from the fungal plant pathogen Fusarium oxysporum.

A retrotransposon from the fungal plant pathogen Fusarium oxysporum f. sp. lycopersici has been isolated and characterized. The element, designated skippy (skp) is 7846 bp in length, flanked by identical long terminal repeats (LTR) of 429 bp showing structural features characteristic of retroviral and retrotransposon LTRs. Target-site duplications of 5 bp were found. Two long overlapping open reading frames (ORF) were identified. The first ORF, 2562 bp in length, shows homology to retroviral gag genes. The second ORF, 3888 bp in length, has homology to the protease, reverse transcriptase. RNase H and integrase domains of retroelement pol genes in that order. Sequence comparisons and the order of the predicted proteins from skippy indicate that the element is closely related to the gypsy family of LTR-retrotransposons. The element is present in similar copy numbers in the two races investigated, although RFLP analysis showed differences in banding patterns. The number of LTR sequences present in the genome is higher than the number of copies of complete elements, indicating excision by homologous recombination between LTR sequences.

Amino Acid Sequence↗
PubMed1994

IS231 and other Bacillus thuringiensis transposable elements: a review.

Bacillus thuringiensis is an entomopathogenic bacterium whose toxicity is due to the presence in the sporangia of delta-endotoxin crystals active against agricultural pests and vectors of human and animal diseases. Most of the genes coding for these toxin proteins are plasmid-borne and are generally structurally associated with insertion sequences (IS231, IS232, IS240, ISBT1 and ISBT2) and transposons (Tn4430 and Tn5401). Several of these mobile elements have been shown to be active and are believed to participate in the crystal gene mobility, thereby contributing to the variation of bacterial toxicity. Structural analysis of the iso-IS231 elements indicates that they are related to IS1151 from Clostridium perfringens and distantly related to IS4 and IS186 from Escherichia coli. Like the other IS4 family members, they contain a conserved transposase-integrase motif found in other IS families and retroviruses. Moreover, functional data gathered from IS231A in Escherichia coli indicate a non-replicative mode of transposition, with a marked preference for specific targets. Similar results were also obtained in Bacillus subtilis and B. thuringiensis, and a working model for DNA-protein interactions at the target site is proposed.

Amino Acid Sequence↗
PubMed1995

Analysis of the phylogenetic placement of different spumaretroviral genes reveals complex pattern of foamy virus evolution.

Foamy or spumaviruses are complex retroviruses. Phylogenetic trees have been constructed previously for either the polymerase or integrase domains showed a clustering of the foamy viruses relatively distant from other retroviruses. The most related retrovirus was found to be murine leukemia virus, irrespective of the method used or foamy viral gene analyzed. We analyze bel genes of different foamy viruses and compared the corresponding phylogenetic trees with those obtained from the pol genes that were constructed with refined computer programs. In addition, the nucleocapsid protein sequence of foamy viruses was used for a comparative phylogenetic analysis. Known biological properties of the individual FV protein domains are discussed to ascertain the apparent phylogenetic relatedness.

Amino Acid Sequence↗
PubMed1996

A retrotransposon-like sequence linked to the S-locus of Nicotiana alata is expressed in styles in response to touch.

We have identified a family of repetitive sequences in the genome of Nicotiana alata named Tna1 (Transposon of N. alata). The first element we characterised was a genomic clone for the N. alata s6-ribonuclease (S6-RNase), a gene required for self-incompatibility in this species. The DNA sequence of this element resembles the integrase domain of retrotransposons of the gypsy class and is most similar to a retrotransposon from Lilium henryi. A transcript present in N.alata styles (self-incompatibility genotype S6S6) hybridized to Tna1 and accumulated in the style following either pollination or touching. This transcript was cloned from a cDNA library and was encoded by second, partial Tna1 elements. Neither the transcribed sequence nor the original Tna1 element contain an open reading frame or is likely to be able to transpose. The second element was mapped using a population of N.alata plants segregating for alleles of the self-incompatibility locus and is closely linked to the S6-allele. The Tna1 element is present in a number of Nicotiana species and appears to have been active at least twice during the evolution of this genus.

Amino Acid Sequence↗