Resetting the Site: Redirecting Integration of an Insertion Sequence in a Predictable Way

Guynet, Catherine; Achard, Adeline; Hoang, Bao Ton; Barábas, O.; Hickman, A.B.; Dyda, F.; Chandler, Michaël

doi:10.1016/j.molcel.2009.05.017

Cited by 31 publications

(40 citation statements)

References 22 publications

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“…It was initially believed that TE show no or only low sequence specificity in their target choice. For example IS630 and the eukaryotic Tc/mariner families (Tellier et al, this volume) both require a TA dinucleotide in the target (36,37) whereas others such as the IS200/IS605 and IS91 families require short tetra-or penta-nucleotide sequences (94,95). Yet others, such as IS1 and IS186 (of the IS4 family), show some regional specificity (for AT-rich and GC-rich sequences, respectively) (96)(97)(98).…”

Section: Target Choicementioning

confidence: 99%

“…The IS200/IS605 transposition mechanism is well understood from a combination of genetic, biochemical and structural studies (94,100,245,(250)(251)(252)(253)(254)(255). Briefly, it occurs using a single-strand "peel-and-paste" mechanism (He et al, this volume) in which a specific single transposon strand (the "top" strand) is excised to form a single-strand transposon circle.…”

Section: (Ii) Mechanismmentioning

confidence: 99%

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Everyman's Guide to Bacterial Insertion Sequences

et al. 2015

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The number and diversity of known prokaryotic insertion sequences (IS) have increased enormously since their discovery in the late 1960s. At present the sequences of more than 4000 different IS have been deposited in the specialized ISfinder database. Over time it has become increasingly apparent that they are important actors in the evolution of their host genomes and are involved in sequestering, transmitting, mutating and activating genes, and in the rearrangement of both plasmids and chromosomes. This review presents an overview of our current understanding of these transposable elements (TE), their organization and their transposition mechanism as well as their distribution and genomic impact. In spite of their diversity, they share only a very limited number of transposition mechanisms which we outline here. Prokaryotic IS are but one example of a variety of diverse TE which are being revealed due to the advent of extensive genome sequencing projects. A major conclusion from sequence comparisons of various TE is that frontiers between the different types are becoming less clear. We detail these receding frontiers between different IS-related TE. Several, more specialized chapters in this volume include additional detailed information concerning a number of these.In a second section of the review, we provide a detailed description of the expanding variety of IS, which we have divided into families for convenience. Our perception of these families continues to evolve and families emerge regularly as more IS are identified. This section is designed as an aid and a source of information for consultation by interested specialist readers.

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Section: Target Choicementioning

confidence: 99%

Section: (Ii) Mechanismmentioning

confidence: 99%

Everyman's Guide to Bacterial Insertion Sequences

et al. 2015

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“…This reorganization of DNA segments results in an integrated transposon. One consequence of this mechanism is that the integration site-specificity can be manipulated at will by simply changing the bases comprising the guide sequence (168).…”

Section: Huh Transposases (I) Transposon End Recognitionmentioning

confidence: 99%

Mechanisms of DNA Transposition

Hickman

Dyda

2015

Microbiol Spectr

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DNA transposases use a limited repertoire of structurally and mechanistically distinct nuclease domains to catalyze the DNA strand breaking and rejoining reactions that comprise DNA transposition. Here, we review the mechanisms of the four known types of transposition reactions catalyzed by (1) RNase H-like transposases (also known as DD(E/D) enzymes); (2) HUH single-stranded DNA transposases; (3) serine transposases; and (4) tyrosine transposases. The large body of accumulated biochemical and structural data, particularly for the RNase H-like transposases, has revealed not only the distinguishing features of each transposon family, but also some emerging themes that appear conserved across all families. The more-recently characterized single-stranded DNA transposases provide insight into how an ancient HUH domain fold has been adapted for transposition to accomplish excision and then site-specific integration. The serine and tyrosine transposases are structurally and mechanistically related to their cousins, the serine and tyrosine site-specific recombinases, but have to date been less intensively studied. These types of enzymes are particularly intriguing as in the context of site-specific recombination they require strict homology between recombining sites, yet for transposition can catalyze the joining of transposon ends to form an excised circle and then integration into a genomic site with much relaxed sequence specificity.In this chapter, we provide an overview of the fundamental concepts of DNA transposition mechanisms. Our aim is to emphasize basic themes and, in this effort, we will focus on specific illustrative cases rather than attempt an exhaustive review of the literature. We hope that the selected references will point the curious reader towards the landmark studies in the field as well as some of the most exciting recent results. We also direct the reader to other recent reviews (1-3).DNA transposases are enyzmes that move discrete segments of DNA called transposons from one location in the genome (often called the donor site) to a new site without using RNA intermediates. DNA transposases are usually encoded by the mobile element itself (in which case they are "autonomous" transposons). However, some transposons are missing a self-encoded transposase yet have ends that can be recognized by a transposase encoded somewhere else in the genome, and thus are "non-autonomous" (Siguier et al., this volume). Although logic suggests that all DNA transposons are moved by transposases, the term was originally reserved for those enzymes that do not require significant regions of homology between any part of the transposon and the sites to which they are moved, the so-called target (or insertion or integration) sites. As biology is not always neat and tidy, transposases can exhibit a spectrum of homology requirements and vagaries of terminology have arisen such that certain transposases are sometimes referred to as "resolvases" or by the generic term "recombinases".From a mechanistic perspective, t...

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“…A deeper understanding of the detailed mechanism of IS transposition may allow us to conceive of redirecting insertion specificity in a predictable way (Guynet et al 2009), or instead, pave the way for the design of safer and more evolutionary robust genetic circuits. Our results with bench-scale bioreactors also raise important issues and concerns on the safety of DNA-based therapeutics upon amplification at a larger scale.…”

Section: Discussionmentioning

confidence: 99%

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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Resetting the Site: Redirecting Integration of an Insertion Sequence in a Predictable Way

Cited by 31 publications

References 22 publications

Everyman's Guide to Bacterial Insertion Sequences

Everyman's Guide to Bacterial Insertion Sequences

Mechanisms of DNA Transposition

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

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