Target DNA Bending is an Important Specificity Determinant in Target Site Selection in Tn10 Transposition

Pribil, Patrick; Haniford, David B.

doi:10.1016/s0022-2836(03)00588-6

Cited by 48 publications

(56 citation statements)

References 45 publications

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“…More recent work has shown that the deformability of certain sequences can be of prime importance for transposable elements from highly divergent organisms (21,40). Molecular dissection of Tn10 target site selection has revealed that the ability of the transposase to alter a potential target sequence can be a critical component of target site selection (32). We have found that primary sequence cannot explain Tn917's penchant for the terminus region.…”

Section: Discussionmentioning

confidence: 78%

Construction of anEnterococcus faecalisTn917-Mediated-Gene-Disruption Library Offers Insight into Tn917Insertion Patterns

et al. 2004

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Sequencing the insertion sites of 8,865 Tn917 insertions in Enterococcus faecalis strain OG1RF identified a hot spot in the replication terminus region corresponding to 6% of the genome where 65% of the transposons had inserted. In E. faecalis, Tn917 preferentially inserted at a 29-bp consensus sequence centered on TATAA, a 5-bp sequence that is duplicated during insertion. The regional insertion site preference at the chromosome terminus was not observed in another low-G؉C gram-positive bacterium, Listeria monocytogenes, although the consensus insertion sequence was the same. The 8,865 Tn917 insertion sites sequenced in E. faecalis corresponded to only ϳ610 different open reading frames, far fewer than the predicted number of 2,400, assuming random insertion. There was no significant preference in orientation of the Tn917 insertions with either transcription or replication. Even though OG1RF has a smaller genome than strain V583 (2.8 Mb versus 3.2 Mb), the only E. faecalis strain whose sequence is in the public domain, over 10% of the Tn917 insertions appear to be in a OG1RF-specific sequence, suggesting that there are significant genomic differences among E. faecalis strains.

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Section: Discussionmentioning

confidence: 78%

Construction of anEnterococcus faecalisTn917-Mediated-Gene-Disruption Library Offers Insight into Tn917Insertion Patterns

et al. 2004

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“…Both minicircle junction and IS2 target sites were shown to adopt similar intrinsically curved structures, supporting the idea that a particular configuration is needed to regulate transposition by promoting the assembly of the transpososome (Lewis et al 2012). In fact, a growing body of evidence has yielded similar observations in other MGEs such as IS10 (Kobori et al 2009), IS231 (Hallet et al 1994), Tn10 (Pribil and Haniford 2003) , bacteriophage Mu, and Tn5 (reviewed in (Nagy and Chandler 2004)). …”

Section: Introductionmentioning

confidence: 65%

Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters

Gonçalves

Oliveira

Gomes

et al. 2014

Appl Microbiol Biotechnol

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Insertion specificity of mobile genetic elements is a rather complex aspect of DNA transposition, which, despite much progress towards its elucidation, still remains incompletely understood. We report here the results of a metaanalysis of IS2 target sites from genomic, phage, and plasmid DNA and find that newly acquired IS2 elements are consistently inserted around abrupt DNA compositional shifts, particularly in the form of switch sites of GC skew. The results presented in this study not only corroborate our previous observations that both the insertion sequence (IS) minicircle junction and target region adopt intrinsically bent conformations in IS2, but most interestingly, extend this requirement to other families of IS elements. Using this information, we were able to pinpoint regions with high propensity for transposition and to predict and detect, de novo, a novel IS2 insertion event in the 3′ region of the gfp gene of a reporter plasmid. We also found that during amplification of this plasmid, process parameters such as scale, culture growth phase, and medium composition exacerbate IS2 transposition, leading to contamination levels with potentially detrimental clinical effects. Overall, our findings provide new insights into the role of target DNA structure in the mechanism of transposition of IS elements and extend our understanding of how culture conditions are a relevant factor in the induction of genetic instability.

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“…Indeed, the activity of integrase genes found in several genomic islands and involved in genomic islands mobility is likely to depend upon the DNA structure (Cali et al, 2004;Hochhut et al, 2006;Lesic et al, 2004;Pribil & Haniford, 2003;Radman-Livaja et al, 2006). Interestingly, several tDNA loci with high scores such as alaX, glyY, lysQ, proM, thrT, valW or glnX had DNA curvature profiles different from those of a number of loci with low scores such as asn loci, pheU, metV, pheV and serW.…”

Section: Discussionmentioning

confidence: 99%

tDNA locus polymorphism and ecto-chromosomal DNA insertion hot-spots are related to the phylogenetic group of Escherichia coli strains

et al. 2007

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tRNA-encoding genes (tDNA) are known hot-spots for the integration of ecto-chromosomal DNA (ECDNA) including genomic islands. However, only a few loci are currently known to be targeted by such insertions in Escherichia coli. A PCR-based screening of tDNA integrity was therefore performed on a collection of E. coli strains in order to identify tDNA loci that are most frequently intact and those that are preferred ECDNA insertion sites. It was shown that only a subset of tDNAs were hot-spots for ECDNA insertions, and that the majority of loci were never targeted by such insertions. Polycistronic tDNAs, highly transcribed tDNAs or tDNAs encoding tRNAs recognizing frequently used codons were generally not targeted by ECDNA insertions. Most interestingly, strains of different ECOR groups showed different patterns of tDNA loci polymorphism. More subtle differences were also observed between strains of different pathotypes.

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Target DNA Bending is an Important Specificity Determinant in Target Site Selection in Tn10 Transposition

Cited by 48 publications

References 45 publications

Construction of anEnterococcus faecalisTn917-Mediated-Gene-Disruption Library Offers Insight into Tn917Insertion Patterns

Construction of anEnterococcus faecalisTn917-Mediated-Gene-Disruption Library Offers Insight into Tn917Insertion Patterns

Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters

tDNA locus polymorphism and ecto-chromosomal DNA insertion hot-spots are related to the phylogenetic group of Escherichia coli strains

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