Involvement of multiple translocating DNA segments and recombinational hotspots in the structural evolution of bacterial plasmids

Kopecko, Dennis J.; Brevet, Jean; Cohen, Stanley N.

doi:10.1016/s0022-2836(76)80124-6

Cited by 142 publications

(61 citation statements)

References 44 publications

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“…The 66 rightside flanking nucleotides in Fig. 2B (11,17) and may in all cases be due in part to the presence of similar sequences in the incoming and target transposon. For example, Tdd-2 and Tdd-3 have a 22-bp sequence at one end in common but are otherwise unrelated.…”

Section: Discussionmentioning

confidence: 99%

Structure and unusual characteristics of a new family of transposable elements in the sea urchin Strongylocentrotus purpuratus.

Cohen¹,

Hoffman-Liebermann²,

Kedes³

1985

Mol. Cell. Biol.

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The transposable element family TU of the sea urchin Strongylocentrotus purpuratus, a higher eucaryote, has recently been described (D. Liebermann, B. Hoffman-Liebermann, J. Weinthal, G. Childs, R. Maxson, A. Mauron, S. N. Cohen, and L. Kedes, Nature [London] 306:342-347, 1983). A member of this family, TU4, has an insertion, called ISTU4, of non-TU DNA. ISTU4 is a member of a family of repetitive sequences, which are present in some 1,000 copies per haploid S. purpuratus genome (B. Hoffman-Liebermann, D. Liebermann, L. H. S. N. Cohen, Mol. Cell. Biol. 5:991-1001, 1985). We analyzed this insertion to determine whether it is itself a transposable element. The nucleotide sequence of ISTU4 was determined and showed an unusual structure. There are four, -150 nucleotides long, imperfect direct repeats followed by a single truncated version of these repeats. This region is bounded at either side by -100-nucleotide-long sequences that are not related to each other or to the repeats. Nucleotide sequences at the boundaries of ISTU4-homologous and flanking regions in five genomic clones show that ISTU4 represents a family of sequences with discrete ends, which we call Tsp elements. We showed that the genomic locus that carries a Tsp element in one individual was empty in other individuals and conclude that Tsp elements are a new and different type of transposable element. Tsp elements lack two features common to most other transposable elements: Tsp integration does not result in the duplication of host DNA, and there are no inverted repeats at their termini, although short inverted repeats are present at a distance from the termini.Transposable elements have been well studied at the molecular level in a variety of organisms, such as Escherichia coli and other bacteria, maize, yeast, and various Drosophila species (3,8,10). In these systems transposable elements may often have a profound influence on expression of nearby structural genes. The elements can not only inactivate normally active genes but also activate silent genes or alter the level of expression of active ones. This report describes a new family of transposable elements, which we have named Tsp elements, in the genome of the sea urchin Strongylocentrotus purpuratus. The Tsp family was discovered because one of its members is inserted within a member of the TU transposable element family (9).A number of features of the TU family are relevant to an understanding of the present paper. TU elements are transposable elements present in some 400 copies in the genome of the sea urchin species S. purpuratus. This family was originally identified because one of its members, TU1, had integrated into a histone H2B processed pseudogene (12). Subsequent work has extensively characterized the TU family of transposable elements (9, 12). TU elements fall into several classes. A major class (-40%), of which TUl is an example, is rather uniform in structure. The elements of this class consist of several domains (see Fig. 1, upper panel). The termini of the elements are formed...

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Section: Discussionmentioning

confidence: 99%

Structure and unusual characteristics of a new family of transposable elements in the sea urchin Strongylocentrotus purpuratus.

Cohen¹,

Hoffman-Liebermann²,

Kedes³

1985

Mol. Cell. Biol.

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“…The modularity of the TU element family is reminiscent of the structure of some procaryotic transposons (34) and suggests a possible role for these elements in the dispersion and rearrangement of segments of genomic DNA.…”

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confidence: 99%

TU elements: a heterogeneous family of modularly structured eucaryotic transposons.

Hoffman-Liebermann¹,

Liebermann²,

Kedes³

et al. 1985

Mol. Cell. Biol.

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We describe here a family of foldback transposons found in the genome of the higher eucaryote, the sea urchin Strongylocentrotus purpuratus. Two major classes of TU elements have been identified by analysis of genomic DNA and TU element clones. One class consists of largely similar elements with long terminal inverted repeats (IVRs) containing outer and inner domains and sharing a common middle segment that can undergo deletions. Some of these elements contain insertions. The second class is highly heterogeneous, with many different middle segments nonhomologous to those of the first-class and variable-sized inverted repeats that contain only an outer domain. The middle and insertion segments of both classes carry sequences that also are found unassociated from the inverted repeats at many other genomic locations. We conclude that the TU elements are modular structures composed of inverted repeats plus other sequence domains that are themselves members of different families of dispersed repetitive sequences. Such modular elements may have a role in the dispersion and rearrangement of genomic DNA segments.Transposable genetic elements, which were first discovered in maize (41) and later found in bacteria (for a review, see reference 32), have been identified in a variety of animal species (52). There is increasing evidence that transposable elements may play an important role in generating genetic diversity (16). Moreover, in yeast cells, the regulation of the mating-type cassette switch involves site-specific recombinational events similar to those mediated by transposons (24, 31), as does the mechanism regulating the variant expression of surface antigens in trypanosomes (5). In Drosophila melanogaster, hybrid dysgenesis involves the P transposable element (30). Similar rearrangements have been postulated to play a role in the regulation of cell type determination and differentiation (26,42). Recent themselves members of different families of dispersed repetitive sequences. The modularity of the TU element family is reminiscent of the structure of some procaryotic transposons (34) and suggests a possible role for these elements in the dispersion and rearrangement of segments of genomic DNA. MATERIALS AND METHODSGeneral methods. Restriction enzymes were obtained from New England Biolabs or Bethesda Research Laboratories and used according to the instructions of the manufacturers. DNA fragments were isolated by electroelution from either agarose or acrylamide preparative gels after fractionation of the appropriately digested DNA. Further purification by multiple phenol, phenol-chloroform, and chloroform extractions was followed by precipitation with ethanol and resuspension in a small volume (50 to 100 ,ul) of doubly distilled water. Fragments used as hybridization probes were radioactively labeled by nick translation (48). Both acrylamide and agarose gels were run in TBE buffer (0.089 M Tris-borate [pH 8.3], 20 mM EDTA). Fragments of k HindlIl-and pBR322 HinfI-digested DNA were used as molecular weight standar...

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“…3) (18). Indeed, Kopecko et al (34) suggested that the termini of several transposons can serve as hot spots for recombination of plasmid DNA. The determinants of this specificity are not known, but it seems likely that the sequences related to the ends of transposons provide a preferred substrate for transposases (5,23).…”

Section: Discussionmentioning

confidence: 99%

The dehalogenase gene dehI from Pseudomonas putida PP3 is carried on an unusual mobile genetic element designated DEH

1992

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As a result of the production of two dehalogenases (DehI and Dehll), Pseudomonas putida PP3 utilized halogenated alkanoic acids, such as 2-monochloropropionic acid (2MCPA), as sole sources of carbon and energy. The DehI gene (dehl) was carried on a mobile genetic element (DEH) located on the chromosome of strain PP3. DEH recombined with target plasmid DNAs at high frequencies (e.g., 3.8 X 10-4 per RP4.5 plasmid transferred). The regulated expression ofdehI was detected in P. putida, Pseudomonas aeruginosa, and Escherichia coli strains containing derivative plasmids of RP4.5 and pWWO recombined with DEH. Movement of DEH from the unstable RP4 derivatives pNJ5000 and pMR5 resulted in the insertion of DEH into the chromosome of RecA+ strains ofP. putida but not in RecA+ nor RecA-strains ofE. coli. Rescue ofDEH from the chromosome ofP. putida KT2441 onto plasmid RP4 involved recombination at a frequency (2.7 x 10-4 per RP4 plasmid transferred) comparable to that observed in strain PP3. The DEH element was not classified as a conventional transposon because it did not move as a discrete DNA fragment: dehl-containing inserts in plasmid DNA targets varied in size between 6 and 13 kb. In addition, DEH exhibited a marked preference for insertion into a specific site on the plasmid pWWO, but its transposition, independent of host recombinational systems, remains to be demonstrated. However, the transposonlike characteristics of DEH included the conservation of restriction endonuclease sites, high-frequency recombination with different target replicons (plasmid and chromosomal DNA), and promiscuous insertion into plasmid RP4-based replicons. Therefore, it is proposed that DEH is an unusual mobile genetic element.Hydrolytic halidohydrolases (dehalogenases) are common in the microbial world. Many dehalogenases, isolated from both prokaryotic and eukaryotic species, have been described which catalyze the dehalogenation of a range of halogenated aromatic and aliphatic compounds (40,56). Recent reports in the literature illustrate the variety of dehalogenases produced by gram-negative bacteria (28,31,52). The majority of dehalogenase-producing bacteria have been obtained by enrichments with soils previously challenged with haloorganic compounds, and usually they are selected by their ability to grow on the enrichment substrate. However, the potential for dehalogenation in microorganisms is also evident in samples from marine and freshwater sediments not exposed to haloorganic compounds (32, 55).Pseudomonas putida PP3 evolved the ability to utilize halogenated alkanoic acids during prolonged continuous flow culture of its parent, P. putida PP1, in the presence of the herbicide Dalapon (2,2-dichloropropionic acid) (44). Mutations associated with acquisition of this phenotype resulted in the inducible expression of two dehalogenases, DehI and DehII, whose genes were designated dehI and dehII (45, 58). The dehalogenases DehI and DehII catalyzed the hydrolytic cleavage of the carbon-halogen bond of C1 to C4 2-halogenated alkanoic aci...

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Involvement of multiple translocating DNA segments and recombinational hotspots in the structural evolution of bacterial plasmids

Cited by 142 publications

References 44 publications

Structure and unusual characteristics of a new family of transposable elements in the sea urchin Strongylocentrotus purpuratus.

Structure and unusual characteristics of a new family of transposable elements in the sea urchin Strongylocentrotus purpuratus.

TU elements: a heterogeneous family of modularly structured eucaryotic transposons.

The dehalogenase gene dehI from Pseudomonas putida PP3 is carried on an unusual mobile genetic element designated DEH

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