Short palindromic repetitive DNA elements in enterobacteria: a survey

Bachellier, Sophie; Clément, Jean-Marie; Hofnung, Maurice

doi:10.1016/s0923-2508(99)00128-x

Cited by 87 publications

(80 citation statements)

References 41 publications

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“…The lac operon of Escherichia coli on plasmid F9 128 was chosen because amplification of this region plays a major role in reversion of lac under selection in the Cairns system (Cairns and Foster 1991;Hendrickson et al 2002;Slechta et al 2003;Kugelberg et al 2006). Like the argH gene, the plasmid lac region is flanked by large repeats (IS3; 1258 bp) and by clusters of shorter (30-bp) Rep elements (Bachellier et al 1999;Kofoid et al 2003). The lac locus is duplicated in $0.2% of cells in an unselected culture.…”

Section: Resultsmentioning

confidence: 99%

Duplication Frequency in a Population of Salmonella enterica Rapidly Approaches Steady State With or Without Recombination

Reams¹,

Kofoid²,

et al. 2010

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Tandem duplications are among the most common mutation events. The high loss rate of duplication suggested that the frequency of duplications in a bacterial population (1/1000) might reflect a steady state dictated by relative rates of formation (k F ) and loss (k L ). This possibility was tested for three genetic loci. Without homologous recombination (RecA), duplication loss rate dropped essentially to zero, but formation rate decreased only slightly and a steady state was still reached rapidly. Under all conditions, steady state was reached faster than predicted by formation and loss rates alone. A major factor in determining steady state proved to be the fitness cost, which can exceed 40% for some genomic regions. Depending on the region tested, duplications reached 40-98% of the steady-state frequency within 30 generations-approximately the growth required for a single cell to produce a saturated overnight culture or form a large colony on solid medium (10 9 cells). Long-term bacterial populations are stably polymorphic for duplications of every region of their genome. These polymorphisms contribute to rapid genetic adaptation by providing frequent preexisting mutations that are beneficial whenever imposed selection favors increases in some gene activity. While the reported results were obtained with the bacterium Salmonella enterica, the genetic implications seem likely to be of broader biological relevance.

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Section: Resultsmentioning

confidence: 99%

Duplication Frequency in a Population of Salmonella enterica Rapidly Approaches Steady State With or Without Recombination

Reams¹,

Kofoid²,

et al. 2010

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“…After replication fork stalling, single strands of nascent DNA are released and contribute to chromosome rearrangement (Lovett 2004). Short (imperfect) palindromic sequences are frequent (Stern et al 1984;Bachellier et al 1999;Vasconcelos et al 2000) and can form ''snap-back'' structures in single-stranded DNA (see Figure 2).…”

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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“…The accessibility of these probes to the 16S rRNA molecule by FISH was also checked according to the ARB software (http,//www.arb-home.de; Kumar et al, 2005). The ERIC-1 probe used in this work (5´-ATGTAAGCTCCTGGGGATTCAC-3´) targets from 42 to 63 bp position of ERIC consensus sequence present in all Enterobacteriaceae (Bachelier et al, 1999;Hulton et al, 1991;Wilson & Sharp, 2006). These probes were covalently labelled at their 5´end with the isothiocyanate derivative (CY3) or with fluorescein isothiocyanate (FITC), and purified by reverse-phase liquid chromatography.…”

Section: Methodsmentioning

confidence: 99%

“…The aim of this work was to develop new probes to detect the main enterobacteria in microbial populations present in the paper mills, in order to evaluate the efficiency of different treatments to eliminate them. Bacterial detection and identification have been carried out by a FISH method that includes two new probes targeted to 16S rRNA and a probe based on the conserved central region of the Enterobacterial Repetitive Intergenic Consensus (ERIC) sequences, which are located at a high copy number in extragenic regions of the Enterobacteriaceae genome (Bachelier et al, 1999;Hulton et al, 1991;Wilson & Sharp, 2006). The viability of these enterobacteria after the chemical treatments was measured by FC.…”

Section: Introductionmentioning

confidence: 99%

Fluorescent in situ hybridization and flow cytometry as tools to evaluate the treatments for the control of slime-forming enterobacteria in paper mills

Torres

Gibello

Nande

et al. 2008

Appl Microbiol Biotechnol

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Short palindromic repetitive DNA elements in enterobacteria: a survey

Cited by 87 publications

References 41 publications

Duplication Frequency in a Population of Salmonella enterica Rapidly Approaches Steady State With or Without Recombination

Duplication Frequency in a Population of Salmonella enterica Rapidly Approaches Steady State With or Without Recombination

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

Fluorescent in situ hybridization and flow cytometry as tools to evaluate the treatments for the control of slime-forming enterobacteria in paper mills

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