Tandem chromosomal duplications: role of REP sequences in the recombination event at the join-point.

Shyamala, Venkatakrishna; Schneider, Erwin; Ames, Giovanna Ferro‐Luzzi

doi:10.1002/j.1460-2075.1990.tb08192.x

Cited by 74 publications

(47 citation statements)

References 43 publications

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“…Interestingly, the truncation maps to the position of the central cleavage site. These results, together with the observations that REPs can recombine with each other by a RecA-independent mechanism (Shyamala et al, 1990) and that DNA gyrase can promote recombination (Miura-Masuda and Ikeda, 1990), indicate that DNA gyrase might play a significant role in the process of dispersion of REP/BIME elements and of rearrangement of the bacterial chromosome through its interaction with BIMEs-2.…”

Section: Discussionmentioning

confidence: 78%

In vivo cleavage of Escherichia coli BIME‐2 repeats by DNA gyrase: genetic characterization of the target and identification of the cut site

Espéli

Boccard

1997

Molecular Microbiology

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SummaryThe Escherichia coli chromosome contains about 300 bacterial interspersed mosaic elements (BIMEs). These elements, located at the 3Ј end of genes, are composed of three types of alternating repetitive extragenic palindromes (REPs). Based on the type of REP they contain and on their ability to interact with the integration host factor (IHF), BIMEs are subdivided into two families: BIME-1 elements contain an IHF binding site flanked by converging Y and Z1 REPs, whereas BIME-2 elements contain a variable number of alternating Y and Z2 REPs without an IHF site. Although some BIMEs have been implicated in the protection of mRNA against 3Ј exonucleolytic degradation, the main role of elements belonging to both families remains to be elucidated. In this paper, we used oxolinic acid, a drug that reveals potential sites of DNA gyrase action, to demonstrate that DNA gyrase interacts in vivo with BIME-2 elements. The frequency of cleavage varied from one element to another, and the cleavage pattern observed in elements containing several REPs indicated that DNA gyrase cut DNA every two REPs. A single cleavage site has been identified in the Y REP in six out of seven instances, and the nucleotide sequence of a 44 bp fragment containing the scission point displayed conserved residues at six positions. The lack of one of the conserved residues accounted for the absence of cleavage in most of the Z2 REPs. Our results also showed that cleaved REPs were always associated with another REP, suggesting that a pair of diverging REPs constitutes the target of DNA gyrase. DNA gyrase cleavage at repetitive BIME-2 elements may have consequences for DNA topology and genomic rearrangements.

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Section: Discussionmentioning

confidence: 78%

In vivo cleavage of Escherichia coli BIME‐2 repeats by DNA gyrase: genetic characterization of the target and identification of the cut site

Espéli

Boccard

1997

Molecular Microbiology

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“…Approximately 40 REP elements are found near lac in seven major (12 total) clusters of headto-head REP dyads (12). Exchanges between REP elements can cause duplications and deletions (12)(13)(14)(15)(16).…”

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confidence: 99%

Multiple pathways of selected gene amplification during adaptive mutation

Kugelberg

Kofoid

Reams

et al. 2006

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

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In a phenomenon referred to as ''adaptive mutation,'' a population of bacterial cells with a mutation in the lac operon (lac ؊ ) accumulates Lac ؉ revertants during prolonged exposure to selective growth conditions (lactose). Evidence was provided that selective conditions do not increase the mutation rate but instead favor the growth of rare cells with a duplication of the leaky lac allele. A further increase in copy number (amplification) improves growth and increases the likelihood of a sequence change by adding more mutational targets to the clone (cells and lac copies per cell). These duplications and amplifications are described here. Before selection, cells with large (134-kb) lac duplications and long junction sequences (>1 kb) were common (0.2%). The same large repeats were found after selection in cells with a low-copy-number lac amplification. Surprisingly, smaller repeats (average, 34 kb) were found in high-copy-number amplifications. The small-repeat duplications form when deletions modify a preexisting large-repeat duplication. The shorter repeat size allowed higher lac amplification and better growth on lactose. Thus, selection favors a succession of gene-amplification types that make sequence changes more probable by adding targets. These findings are relevant to genetic adaptation in any biological systems in which fitness can be increased by adding gene copies (e.g., cancer and bacterial drug resistance).gene duplication ͉ genetic adaptation ͉ natural selection ͉ genome instability ͉ mutation under selection

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“…These studies have led to the proposal that the PU or REP sequence is involved in the folding of the bacterial nucleoid into independent supercoiled looped domains (13,58). The REP sequence has also been implicated in chromosomal rearrangements (12,58) and has been identified at the junction of tandem duplications (57). Any proposed function(s) must explain the conserved primary sequence, conserved palindromic structure, location in noncoding regions, inclusion in transcribed sequences, distribution throughout the bacterial chromosome, presence in different species, and ubiquitous nature of the REP sequence.…”

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confidence: 99%