IS406 and IS407, two gene-activating insertion sequences from Pseudomonas cepacia

Wood, M.; Byrne, Armando M.; Lessie, T G

doi:10.1016/0378-1119(91)90519-h

Cited by 53 publications

(42 citation statements)

References 16 publications

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“…By searching the GenBank/EMBL database with the program TFasta, the putative protein encoded by ORF1 was shown to have significant similarity to the putative transposases of ISRm3 and 10 other IS elements of bacteria. Pairwise comparisons done with the program Gap (Table 2) showed that the putative transposase of ISRm5 is most similar (42.6% identity) to that of IS406 from Pseudomonas cepacia (51).…”

Section: Resultsmentioning

confidence: 99%

Characterization, nucleotide sequence, and conserved genomic locations of insertion sequence ISRm5 in Rhizobium meliloti

Laberge¹,

Middleton²,

Wheatcroft³

1995

J Bacteriol

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A target for ISRm3 transposition in Rhizobium meliloti IZ450 is another insertion sequence element, named ISRm5. ISRm5 is 1,340 bp in length and possesses terminal inverted repeats of unequal lengths (27 and 28 bp) and contain five mismatches. An open reading frame that spans 89% of the length of one DNA strand encodes a putative transposase with significant similarity to the putative transposases of 11 insertion sequence elements from diverse bacterial species, including ISRm3 from R. meliloti. Multiple copies and variants of ISRm5 occur in the R. meliloti genome, often in close association with ISRm3. Five ISRm5 copies in two strains were studied, and each was found to be located between 8-bp direct repeats. At two of these loci, which were shown to be highly conserved in R. meliloti, the copies of ISRm5 were found to be associated with pairs of short inverted repeats resembling transcription terminators. This structural arrangement not only may provide a conserved niche for ISRm5 but also may be a preferred target for transposition.Insertion sequences (IS) are small transposable elements of DNA that are widespread in bacteria (see references 15 and 16 for reviews). They are responsible for various types of genomic modification, including DNA rearrangement, deletion, and duplication. By transposition, they cause insertional mutations which may disrupt genes or modify their transcription. In Rhizobium meliloti, several mutations affecting symbiotic nitrogen fixation with alfalfa (Medicago sativa) have been shown to be the result of spontaneous IS transposition (10,29,33,48). More than 25 distinct IS elements have been found in this species, and it is common for several to occupy the same genome in multiple copies (39, 50). We estimate that most R. meliloti strains carry more than 50 IS copies in total, which, if active in transposition, would be expected to have a considerable effect upon genetic stability. This is consistent with the wide genotypic and phenotypic diversity found within the species generally (11) and in field populations (20,22). As yet, few detailed studies of the IS elements of R. meliloti have been made beyond their distributions and copy numbers. However, it is already clear that there are significant differences in their primary structures and transposition behaviors (10,41,46,47).In this paper, we report the discovery, characterization, and full nucleotide sequence of ISRm5 from R. meliloti IZ450. We describe the structural similarity of two ISRm5-containing loci that are highly conserved in the species. We show that ISRm5 is a target for insertion by ISRm3 (47) and that these IS elements are often closely associated in the R. meliloti genome. ISRm3 and ISRm5 are shown to be structurally distinct elements yet to be related by the similarity of the transposases that they putatively encode. MATERIALS AND METHODSPlasmids, strains, and growth conditions. The bacterial strains and plasmids used in this study are listed in Table 1. R. meliloti and Agrobacterium radiobacter were grown in TY med...

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Section: Resultsmentioning

confidence: 99%

Characterization, nucleotide sequence, and conserved genomic locations of insertion sequence ISRm5 in Rhizobium meliloti

Laberge¹,

Middleton²,

Wheatcroft³

1995

J Bacteriol

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“…Such elements have been implicated in the recruitment of foreign genes for novel catabolic functions (15,43,54,60). Although there is considerable information about the biochemical activities of P. cepacia (2,3,11,25,26,35,40,45,51) and although certain genes and IS elements have been isolated and characterized (5,7,10,15,16,33,36,42,54,59,61), little is known about the overall organization of genes or the genomic distribution of IS elements. To gain such information we undertook the construction of a macrorestriction map of the genome of P. cepacia 17616 by using recently developed techniques for the manipulation of large DNA fragments (8,17,19,(46)(47)(48) To test the phenotypes of auxotrophic strains, 0.5% potassium phthalate or mannitol was substituted for the yeast extract and the medium was supplemented with 50 jig of each required amino acid per ml.…”

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confidence: 99%

Multiple replicons constituting the genome of Pseudomonas cepacia 17616

1994

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Macrorestriction fragment analysis of DNA from Pseudomonas cepacia 17616, in conjunction with Southern hybridization experiments using junction fragments containing rare restriction enzyme sites as probes, indicated that this bacterium contains three large circular replicons of 3.4, 2.5, and 0.9 megabases (Mb). Inclusion of the 170-kb cryptic plasmid present in this strain gave an overall estimate of genome size of 7 Mb. Other Southern hybridization experiments indicated that the three large replicons contained rRNA genes as well as insertion sequence elements identified previously in this strain. The distribution of Swal, PacI, and Pmel sites on the three replicons was determined. A derivative of TnS-751 carrying a SwaI site was used to inactivate and map genes on the 2.5-and 3.4-Mb replicons. Mutants were isolated in which the 2.5-and 0.9-Mb replicons had been reduced in size to 1.8 and 0.65 Mb, respectively. The loss of DNA from the 2.5-Mb replicon was associated with lysine auxotrophy, P-lactamase deficiency, and failure to utilize ribitol and trehalose as carbon and energy sources. DNA fragments corresponding in size to randomly linearized forms of the different replicons were detected in unrestricted DNA by pulsed-field gel electrophoresis. The results provide a framework for further genetic analysis of strain 17616 and for evaluation of the genomic complexities of other P. cepacia isolates.Pseudomonas cepacia has attracted attention because of its extraordinary biodegradative abilities and its potential as an agent of bioremediation (2,13,22,25,35,44,45,51,56). The genome of this bacterium contains a large number of insertion sequences (ISs) (25, 27), which were identified on the basis of their abilities to promote genomic rearrangements (4, 12) and to activate the expression of neighboring genes (15,43,60). Such elements have been implicated in the recruitment of foreign genes for novel catabolic functions (15,43,54,60). Although there is considerable information about the biochemical activities of P. cepacia (2,3,11,25,26,35,40,45,51) and although certain genes and IS elements have been isolated and characterized (5,7,10,15,16,33,36,42,54,59,61), little is known about the overall organization of genes or the genomic distribution of IS elements. To gain such information we undertook the construction of a macrorestriction map of the genome of P. cepacia 17616 by using recently developed techniques for the manipulation of large DNA fragments (8,17,19,(46)(47)(48) To test the phenotypes of auxotrophic strains, 0.5% potassium phthalate or mannitol was substituted for the yeast extract and the medium was supplemented with 50 jig of each required amino acid per ml. For growth in liquid medium, 10-to 20-ml cultures were shaken in 125-ml flasks. For growth on plates, the medium was supplemented with 2% (wt/vol) agar. Preparation of genomic DNA for pulsed-field gel electrophoresis (PFGE). Agarose plugs containing intact chromosomal DNA were prepared essentially as described by Smith and Cantor (47). Approximatel...

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“…Particularly striking is the presence of an inversely repeated 6-bp sequence, 5'-TGTAAA-3', located 20 bp in from both the left and right termini of these elements. All the inserted elements are flanked by an 8-bp direct repeat of the target site (1,23) (Fig. 2).…”

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confidence: 99%

Characterization of IS905, a new multicopy insertion sequence identified in lactococci

1994

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IS406 and IS407, two gene-activating insertion sequences from Pseudomonas cepacia

Cited by 53 publications

References 16 publications

Characterization, nucleotide sequence, and conserved genomic locations of insertion sequence ISRm5 in Rhizobium meliloti

Characterization, nucleotide sequence, and conserved genomic locations of insertion sequence ISRm5 in Rhizobium meliloti

Multiple replicons constituting the genome of Pseudomonas cepacia 17616

Characterization of IS905, a new multicopy insertion sequence identified in lactococci

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