Deletions and DNA rearrangements within the transposable DNA element IS2. A model for the creation of palindromic DNA by DNA repair synthesis

Besemer, J; Görtz, Gabriele; Charlier, Daniël

doi:10.1093/nar/8.23.5825

Cited by 12 publications

(6 citation statements)

References 18 publications

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“…Duplications of DNA sequences between repeats have been noted (22), and duplications and other complex rearrangements have been observed in association with palindromic DNA sequences (23)(24)(25)(26)(27). We have discussed duplication events in more detail elsewhere (9).…”

Section: Discussionmentioning

confidence: 99%

Structural intermediates of deletion mutagenesis: a role for palindromic DNA.

Glickman¹,

Ripley²

1984

Proc. Natl. Acad. Sci. U.S.A.

213

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A model is presented for deletion mutations whose formation is mediated by palindromic and quasipalindromic DNA sequences. It proposes that the self-complementarity of palindromes allows the formation of DNA secondary structures that serve as deletion intermediates. The structures juxtapose the end points of the deletion and thus direct deletion specificity. While misaligned DNA intermediates that explain deletion termini occurring in repeated DNA sequences have been described, no explanations have been offered for deletion termini occurring in other sequences. The DNA secondary structures whose formation is mediated by palindromic sequences appear to explain many of these. In this paper, secondary-structure intermediates are described for a series of spontaneous deletions of known sequence in the lad gene of Escherichia coli. The model is supported by its failure to predict structures that can juxtapose simulated deletion termini in the lacI gene. We have found a strong association between palindromic sequences and repeated sequences at lacl deletion termini that suggests the joint participation of repeated and palindromic DNA sequences in the formation of some deletions. Sequences of deletions in other organisms also suggest the participation of palindromic DNA sequences in the formation of deletions.Local DNA sequences can strongly influence the frequency of mutation (1). The frequent association of deletion termini with repeated DNA sequences (2-4) suggests that deletion mutations are no exception. The In its simplest form, our model proposes that DNA secondary structures whose formation is potentiated by palindromic or quasipalindromic DNA sequences participate in deletion formation through the juxtaposition of deletion end points. The inherent self-complementarity of palindromic DNA sequences permits the formation of cruciform or hairpin structures in nucleic acids, precisely juxtaposing otherwise distant bases (6). Repeated DNA sequences are not required.The termini of the E. coli lacd deletion S86 cannot be juxtaposed by a misalignment involving repeated sequences. However, the deletion termini are located precisely at the ends of a quasipalindromic DNA sequence that includes the entire deletion. The formation of a DNA hairpin or cruciform structure in the wild-type DNA sequence places the deletion termini immediately adjacent to one another, rather than separated by their normal linear distance of 27 base pairs (Fig. 1A). This structural intermediate would produce the S86 deletion if it served as a substrate for excision or as a template for DNA synthesis (Fig. 1B). The latter process might be mediated by either DNA polymerase or DNA ligase. A ligation across such a hairpin stem might also be responsible for deletions if the hairpin served as a substrate for nucleases that removed aberrantly aligned regions from ordinary double-stranded DNA. Whatever the precise molecular mechanism(s) responsible for the production of deletions from such DNA structures, the prediction of the model is that the ...

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Section: Discussionmentioning

confidence: 99%

Structural intermediates of deletion mutagenesis: a role for palindromic DNA.

Glickman¹,

Ripley²

1984

Proc. Natl. Acad. Sci. U.S.A.

213

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“…Apparently, the integration of IS50 in front of the Kmr gene inactivated its expression, presumably by separating it from its promoter, and it was reactivated by the post-transpositional point mutation within the IS50 element. Spontaneous mutations at the end of IS2, integrated in the control region of the gal operon of E. coli, which generate new promoters which give constitutive expression of the operon, are other examples of such post-transpositional modulation of gene function Saedler, 1978, 1979;Sommer et al, 1979;Ahmed et al, 1980;Besemer et al, 1980). They are thought to be the results of small duplications and subsequent small DNA rearrangements associated with DNA replication or repair.…”

Section: Discussionmentioning

confidence: 99%

Phenotypic reversion of an IS1-mediated deletion mutation: a combined role for point mutations and deletions in transposon evolution.

Lida¹,

Marcoli²,

Bickle³

1982

The EMBO Journal

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We have physically characterised a deletion mutant of the R plasmid R100 which has lost all of the antibiotic resistances, including chloramphenicol resistance (Cmr), coded by its IS1‐flanked r‐determinant. The deletion was mediated by one of the flanking IS1 elements and terminates within the carboxyl terminus of the Cmr gene. DNA sequence analysis showed that the mutated gene would produce a protein 20 amino acids longer than the wild‐type due to fusion with an open reading frame in the IS element. Surprisingly for a deletion mutation, rare, spontaneous Cmr revertants could be recovered. Two of the four revertants studied had frame shifts due to the insertion of a single AT base pair at the same position; the revertants would code for a protein five amino acids shorter than the wild‐type. The other two revertants had acquired duplications of the 34‐bp inverted terminal repeat sequences of the IS1 element and would direct the synthesis of a protein six amino acids longer than the wild‐type. The reverted Cmr markers were still capable of transposition. These observations suggest a role for point mutations and small DNA rearrangements in the formation of new gene organisations produced by mobile genetic elements.

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“…Such a structure for promoting constitutive gal expression is apparently not unique. Besemer et al (19) have reported an identical structure for an independently isolated Gal+ revertant of galOP-308, designated gLj-308C-1-0. Interestingly, the Gal-constitutive phenotype of galC200 is retained even when most of the IS2 DNA has been removed by a deletion called t31 (22).…”

Section: Introductionmentioning

confidence: 96%

“…In addition to the insertion of IS2 in orientation II, genes downstream from the insertion of altered IS2(I) sequences may also be expressed constitutively (3,(16)(17)(18)(19). Several such IS2(I) derivatives have been obtained by selection of spontaneous Gal+ pseudo-revertants from the Galstrains, gal3::IS2(I) (9) and 1LOP-308::IS2(I) (1,2).…”

Section: Introductionmentioning

confidence: 99%

“…These independently isolated Gal7 mutants both have a polar IS2(I) insertion in the galactose operon immediately preceding the start of the galE message (3,15) (Figure 1). DNA sequence analyses of the IS2(I) derivatives of gal3 and galOP-308 have revealed that they all involve DNA insertions or sequence changes located 50 to 100 bp upstream from the IS2(I)-galE junction (3,(19)(20)(21). The mechanism whereby these localized alterations of the polar IS2(I) sequence convert a Gal1 phenotype into Gal-constitutive expression is unclear.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Transcription initiation sites within an IS2insertion in a Gal-constitutive mutant ofEscherichia coli

Hinton

Musso

1982

Nucl Acids Res

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Insertion of the insertion sequence Is2(I) directly before the galE gene of the galactose operon results in a Gal minus phenotype (1, 2). The Gal-constitutive allele galc200 (and its deletion derivative galc200 delta 31) arise from such a Gal minus mutant by the insertion of LS2(II) DNA within the LS2(I) sequence (3). We have transcribed in vitro a DNA template representing the IS2-galE region of galc200 delta 31. Gal-directed transcription initiates at two sites within the IS2(I) sequence, 51 and 52 bp from the IS2-galE junction. The promoter for these transcripts, Pgal200 delta 31, is composed of a novel joint between a -10 region from the IS2(I) DNA and a -35 region contributed by the IS2(II) insertion. No promoters intrinsic to the 121 bp of the IS2(II) sequence also present on the template were detected. The relevance of Pgal200 delta 31 to the Galc phenotype of galc200 and to general mechanisms for the constitutive expression of genes adjacent to IS2 is discussed.

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Deletions and DNA rearrangements within the transposable DNA element IS2. A model for the creation of palindromic DNA by DNA repair synthesis

Cited by 12 publications

References 18 publications

Structural intermediates of deletion mutagenesis: a role for palindromic DNA.

Structural intermediates of deletion mutagenesis: a role for palindromic DNA.

Phenotypic reversion of an IS1-mediated deletion mutation: a combined role for point mutations and deletions in transposon evolution.

Transcription initiation sites within an IS2insertion in a Gal-constitutive mutant ofEscherichia coli

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