Detection and analysis of transpositionally active head-to-tail dimers in three additional Escherichia coli IS elements

Szeverényi, Ildikó; Nagy, Zita; Farkas, Tibor; Olasz, Ferenc; Kiss, János

doi:10.1099/mic.0.26121-0

Cited by 15 publications

(17 citation statements)

References 46 publications

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“…Furthermore, whereas the ORF to the right is a truncated tra5 sequence, the tra5 sequence at the left can produce a full-length ORFAB fusedframe transposase (58). IS150 can generate circles by joining IRs upon production of the fused-frame transposase (90), and particularly, composite transposons that carry single inverted repeats at the left and right borders form stable circles (48). PMU1 also carries a gene for DNA protein HU (himA), which is a nonspecific binder of DNA but prefers binding to bent, kinked, or altered DNA sequences (31) and has a role in recombination through the joining of distant recombination sites (5).…”

Section: Discussionmentioning

confidence: 99%

Living with Genome Instability: the Adaptation of Phytoplasmas to Diverse Environments of Their Insect and Plant Hosts

Bai

Zhang

Ewing³

et al. 2006

J Bacteriol

350

447

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Phytoplasmas ("CandidatusPhytoplasmaThe phylogenetic tree of mollicutes is composed of two major clades that diverged early in evolution (51). One clade contains the orders Acholeplasmatales and Anaeroplasmatales (AAA clade mollicutes), and the other clade contains the orders Mycoplasmatales and Entomoplasmatales (SEM clade mollicutes) (9). Phytoplasmas, formerly known as mycoplasma-like organisms of plants, form a monophyletic group in the order Acholeplasmatales (51) and were recently assigned to a novel genus, "Candidatus Phytoplasma" (41). Approximately 20 phytoplasma phylogenetic groups have been proposed based on 16S rRNA gene sequences, and new branches are continuously being discovered (69,85). Members of the order Acholeplasmatales are distinct from other mollicutes in several ways. For instance, whereas most mollicutes use UGA as a tryptophan codon instead of a stop codon, a feature they share with mitochondria, the acholeplasmas and phytoplasmas retained UGA as a stop codon (80).

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Section: Discussionmentioning

confidence: 99%

Living with Genome Instability: the Adaptation of Phytoplasmas to Diverse Environments of Their Insect and Plant Hosts

Bai

Zhang

Ewing³

et al. 2006

J Bacteriol

350

447

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“…The founding member of the family, IS30, is the best characterized at the mechanistic level (117,(182)(183)(184)(185)(186)(187)(188)(189) and an in vitro transposition system has been developed (190). This 1,221 bp long Escherichia coli element belongs to a growing class of IS known to transpose through an intermediate formed by abutting the IR, donor primed transposon replication.…”

Section: (Iii) Mechanism and Insertion Specificitymentioning

confidence: 99%

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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“…IS30 seems not exceptional in this respect. Accumulating data suggest that numerous IS elements may suit the above requirements (7,9,10,33). Mutations such as deletions removing almost an entire element from the dimer, but leaving the IR-IR junction intact or eliminating the domain of Tpase involved in target selection, might easily establish the primitive form of a new site-specific system (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…This finding supports that mechanistically dissimilar enzymes can perform similar biological functions and suggests that transposition and site-specific recombination may be closer to each other in some respect than was supposed earlier. Further support for this idea may emerge from insertion sequence (IS) elements that form an active junction composed of the inverted repeats (IRs) (7)(8)(9)(10). This IR-IR junction shows similarities in its structure and function to the recombination sites of sitespecific systems.…”

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Site-specific recombination by the DDE family member mobile element IS30transposase

Kiss

Szabó

Olasz

2003

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

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DNA rearrangements carried out by site-specific recombinases and transposases (Tpases) show striking similarities despite the wide spectrum of the catalytic mechanisms involved in the reactions. Here, we show that the bacterial insertion sequence (IS)30 element can act similarly to site-specific systems. We have developed an inversion system using IS30 Tpase and a viable phage, where the integration͞excision system is replaced with IS30. Both models have been proved to operate analogously to their natural counterpart, confirming that a DDE family Tpase is able to fulfill the functions of site-specific recombinases. This work demonstrates that distinction between transposition and site-specific recombination becomes blurred, because both functions can be fulfilled by the same enzyme, and both types of rearrangements can be achieved by the same catalytic mechanisms.I t is now well documented that genetic information can be reshuffled by mobile elements that are usually distinguished as site-specific systems and transposons. Even though the output of their activity can be simplified to insertion, deletion, or inversion of DNA segments, transposition and site-specific recombination are generally regarded as distinct phenomena (1). Classification according to the protein-sequence motifs revealed that some transposases (Tpases) and site-specific recombinases (Recases) with entirely different functions fall within the same family (2-6). This finding supports that mechanistically dissimilar enzymes can perform similar biological functions and suggests that transposition and site-specific recombination may be closer to each other in some respect than was supposed earlier. Further support for this idea may emerge from insertion sequence (IS) elements that form an active junction composed of the inverted repeats (IRs) (7-10). This IR-IR junction shows similarities in its structure and function to the recombination sites of sitespecific systems.The Escherichia coli element, IS30, encoding a Tpase with the well conserved DDE signature (11), belongs to the increasing class of elements that transpose through an intermediate formed by abutted IRs (8). The IR-IR joint bracketing a 2-bp spacer is composed of the 26-bp left and right IR ends (IRL and IRR, respectively) that differ at three positions (12). IR-IR joints occur in both IS dimers and minicircles that can integrate into hot spot sequences or next to other IS30 ends (13-15). Whereas transposition into a hot spot is a conventional way of translocation, which accompanies the resolution of IR-IR junction, targeting an IR end seems more specific for IS30 and generates a new IR-IR joint. The IRs, together with the adjacent IS sequences, are important for the directionality of recombination, because, as always, IRL-IRR junction arises through dimerization or targeting an IR (8, 13, 16). The most frequent reaction has been observed when both donor and target DNA contain an IR-IR junction (13). In this case, the rearrangement is remarkably reversible and resembles site-specific ...

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Detection and analysis of transpositionally active head-to-tail dimers in three additional Escherichia coli IS elements

Cited by 15 publications

References 46 publications

Living with Genome Instability: the Adaptation of Phytoplasmas to Diverse Environments of Their Insect and Plant Hosts

Living with Genome Instability: the Adaptation of Phytoplasmas to Diverse Environments of Their Insect and Plant Hosts

Everyman's Guide to Bacterial Insertion Sequences

Site-specific recombination by the DDE family member mobile element IS30transposase

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