A family of dispersed repetitive extragenic palindromic DNA sequences in E. coli.

Gilson, Éric; Clément, Jean-Marie; Brutlag, Douglas L.; Hofnung, Maurice

doi:10.1002/j.1460-2075.1984.tb01986.x

Cited by 221 publications

(129 citation statements)

References 47 publications

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“…Of these 99, twothirds (64 revertants) had a simple tandem duplication structure described previously . Of these 64 strains, 48 had a 3-to 12-bp SJ, 15 had a 30-base repetitive extragenic palindromic element (Gilson et al 1984) at the junction, and one had a copy of IS3, suggesting that it arose by replicative transposition of the IS3C element. None of the 64 amplifications arising under selection had a join point formed by an exchange between IS3A and IS3C, a duplication type found in .0.1% of cells in the unselected parent culture and diagrammed in the center of Figure 1.…”

Section: Resultsmentioning

confidence: 99%

The Tandem Inversion Duplication inSalmonella enterica: Selection Drives Unstable Precursors to Final Mutation Types

et al. 2010

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During growth under selection, mutant types appear that are rare in unselected populations. Stressinduced mechanisms may cause these structures or selection may favor a series of standard events that modify common preexisting structures. One such mutation is the short junction (SJ) duplication with long repeats separated by short sequence elements: AB*(CD)*(CD)*E (* ¼ a few bases). Another mutation type, described here, is the tandem inversion duplication (TID), where two copies of a parent sequence flank an inverse-order segment: AB(CD)(E9D9C9B9)(CD)E. Both duplication types can amplify by unequal exchanges between direct repeats (CD), and both are rare in unselected cultures but common after prolonged selection for amplification. The observed TID junctions are asymmetric (aTIDs) and may arise from a symmetrical precursor (sTID)-ABCDE(E9D9C9B9A9)ABCDE-when sequential deletions remove each palindromic junction. Alternatively, one deletion can remove both sTID junctions to generate an SJ duplication. It is proposed that sTID structures form frequently under all growth conditions, but are usually lost due to their instability and fitness cost. Selection for increased copy number helps retain the sTID and favors deletions that remodel junctions, improve fitness, and allow higher amplification. Growth improves with each step in formation of an SJ or aTID amplification, allowing selection to favor completion of the mutation process.

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Section: Resultsmentioning

confidence: 99%

The Tandem Inversion Duplication inSalmonella enterica: Selection Drives Unstable Precursors to Final Mutation Types

et al. 2010

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“…The discovery that prokaryotic genomes contain repeated sequences such as the repetitive extragenic palindrome (REP), or palindromic unit (PU) sequence (Higgins et al 1982, Gilson et al 1984, and the enterobacterial repetitive intergenic consensus (ERIC) sequence (Hulton et al 1991) has expanded the molecular biology tools that are available to assess the clonal variability of many bacterial strains including Escherichia coli (Versalovic et al 1991, Dalla-Costa et al 1998). These molecular techniques are based on the use of primers homologous to these sequences that after PCR reaction generate a pattern of amplified bands specific for each isolate (Versalovic et al 1991).…”

Section: Introduction Introduction Introduction Introduction Introducmentioning

confidence: 99%

Typing of avian pathogenic Escherichia coli strains by REP-PCR

et al. 2006

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In the present study the repetitive extragenic palindromic (REP) polymerase chain reaction (PCR) technique was used to establish the clonal variability of 49 avian Escherichia coli (APEC) strains isolated from different outbreak cases of septicemia (n=24), swollen head syndrome (n=14) and omphalitis (n=11). Thirty commensal strains isolated from poultry with no signs of these illnesses were used as control strains. The purified DNA of these strains produced electrophoretic profiles ranging from 0 to 15 bands with molecular sizes varying from 100 bp to 6.1 kb, allowing the grouping of the 79 strains into a dendrogram containing 49 REP-types. Although REP-PCR showed good discriminating power it was not able to group the strains either into specific pathogenic classes or to differentiate between pathogenic and non-pathogenic strains. On the contrary, we recently demonstrated that other techniques such as ERIC-PCR and isoenzyme profiles are appropriate to discriminate between commensal and APEC strains and also to group these strains into specific pathogenic classes. In conclusion, REP-PCR seems to be a technique neither efficient nor universal for APEC strains discrimination. However, the population clonal structure obtained with the use of REP-PCR must not be ignored particularly if one takes into account that the APEC pathogenic mechanisms are not completely understood yet.

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“…The IS3 elements (A, B, and C) are the only large (Ͼ1 kb) sequence elements whose recombination can form a lac duplication. Shorter elements (35 bp) are the repetitive extragenic palindromic (REP) sequences (11), each of which is an imperfect 35-bp palindrome. Approximately 40 REP elements are found near lac in seven major (12 total) clusters of headto-head REP dyads (12).…”

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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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A family of dispersed repetitive extragenic palindromic DNA sequences in E. coli.

Cited by 221 publications

References 47 publications

The Tandem Inversion Duplication inSalmonella enterica: Selection Drives Unstable Precursors to Final Mutation Types

The Tandem Inversion Duplication inSalmonella enterica: Selection Drives Unstable Precursors to Final Mutation Types

Typing of avian pathogenic Escherichia coli strains by REP-PCR

Multiple pathways of selected gene amplification during adaptive mutation

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