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Everyman's Guide to Bacterial Insertion Sequences

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  • Authors: Patricia Siguier1, Edith Gourbeyre2, Alessandro Varani3, Bao Ton-Hoang4, Mick Chandler5
  • Editors: Mick Chandler6, Nancy Craig7
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Laboratoire de Microbiologie et Génétique Moléculaires, CNRS, Toulouse, France; 2: Laboratoire de Microbiologie et Génétique Moléculaires, CNRS, Toulouse, France; 3: Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Univ. Estadual Paulista, Jaboticabal, SP, Brazil; 4: Laboratoire de Microbiologie et Génétique Moléculaires, CNRS, Toulouse, France; 5: Laboratoire de Microbiologie et Génétique Moléculaires, CNRS, Toulouse, France; 6: Université Paul Sabatier, Toulouse, France; 7: Johns Hopkins University, Baltimore, MD
  • Source: microbiolspec April 2015 vol. 3 no. 2 doi:10.1128/microbiolspec.MDNA3-0030-2014
  • Received 06 June 2014 Accepted 29 January 2015 Published 02 April 2015
  • Mick Chandler, mike.chandler@ibcg.biotoul.fr
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  • Abstract:

    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.

  • Citation: Siguier P, Gourbeyre E, Varani A, Ton-Hoang B, Chandler M. 2015. Everyman's Guide to Bacterial Insertion Sequences. Microbiol Spectrum 3(2):MDNA3-0030-2014. doi:10.1128/microbiolspec.MDNA3-0030-2014.

Key Concept Ranking

Mobile Genetic Elements
0.8774387
Bacteria and Archaea
0.73705345
Bacterial Genetics
0.5280679
Holliday Junction Resolvase
0.50714123
0.8774387

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/content/journal/microbiolspec/10.1128/microbiolspec.MDNA3-0030-2014
2015-04-02
2017-11-24

Abstract:

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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Figures

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FIGURE 1

Insertion sequence (IS) families with DDE transposases are distinguished by how the second (“nontransferred”) strand is processed. IS are shown in green, flanking DNA in blue. Cleavage is shown as bold vertical arrows. 3′ OH residues are shown as red circles, replicated DNA is indicated in red. The first column shows initial cleavages which generate the 3′OH of the transferred strand and are subsequently used to attack target DNA (not shown) without prior liberation from the flanking donor DNA. Their transfer generates a forked molecule in which a donor and target strand are joined to the TE at each end and which provides a 3′ OH in the flanking target DNA that can prime replication of the transposable elements (TE). This might be called target primed transposon replication. TE of the Tn and IS families transpose in this way. The second column shows a pathway adopted by the IS family. Here, the nontransferred strand is cleaved two bases within the TE (light green square) before cleavage of the transferred strand, which generates the 3′ OH. Repair of the donor molecule would lead to inclusion of a noncomplementary 2-bp scar or footprint (light green square). This is a cut-and-paste mechanism without TE replication. The third column represents transposition using a hairpin intermediate in which the transferred strand is first cleaved and the resulting 3′ OH then attacks the opposite strand to form a hairpin at the TE ends liberating the TE from flanking donor DNA. This is then hydrolyzed to liberate the final transposition intermediate. This is a cut-and paste mechanism without TE replication. The fourth column shows a “copy out-paste” in mechanism adopted by a large number of IS families. It involves cleavage of one IS end and attack of the opposite end by the liberated 3′ OH, the TE then undergoes replication using the 3′ OH in the donor DNA, a process that might be called donor primed transposon replication. This generates a double-strand DNA transposon circle and regenerates the donor molecule. The circle then undergoes cleavage and insertion. Adapted from references 35 and 259 . doi:10.1128/microbiolspec.MDNA3-0030-2014.f1

Source: microbiolspec April 2015 vol. 3 no. 2 doi:10.1128/microbiolspec.MDNA3-0030-2014
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FIGURE 2

Organization of different insertion sequence (IS) -related derivatives. IS with DDE transposases (Tpases) and their derivatives are shown as blue boxes, terminal inverted repeats as light blue triangles and flanking direct target repeats as red boxes. The Tpase s are shown as black horizontal arrows. Passenger genes are shown as orange boxes and transfer functions (in the case of ICE) are shown as purple boxes. The single-strand IS are indicated with their left (red) and right (blue) subterminal secondary structures indicated. (A) IS organization. From top to bottom: a typical IS with a single Tpase ; an IS in which the Tpase reading frame is distributed over two reading phases and requires frameshifting for expression; and the organization of a typical member of the single-strand IS family IS/IS. (B) Different IS-related TE. From top to bottom: composite transposon Tn with inverted flanking copies of IS (note that the left IS copy is not autonomously transposable); a unit transposon of the Tn family; and an integrative conjugative element (ICE). (C) Relationship between IS, miniature inverted repeat transposable elements (MITE), transporter IS (tIS) and mobile insertion cassettes (MIC). (D) Generation of palindrome-associated transposable elements (PATE) from IS/IS family members. Adapted from references 20 and 43 . doi:10.1128/microbiolspec.MDNA3-0030-2014.f2

Source: microbiolspec April 2015 vol. 3 no. 2 doi:10.1128/microbiolspec.MDNA3-0030-2014
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Tables

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TABLE 1

Characteristics of insertion sequence families

Source: microbiolspec April 2015 vol. 3 no. 2 doi:10.1128/microbiolspec.MDNA3-0030-2014

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