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Chapter 26 : Everyman’s Guide to Bacterial Insertion Sequences

Authors: Patricia Siguier1, Edith Gourbeyre2, Alessandro Varani3, Bao Ton-Hoang4, Michael Chandler5
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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
Content Type: Monograph
Publication Year: 2015

Category: Clinical Microbiology

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Abstract:

We have divided this review into two major sections. In one, we have attempted to present an overview of our current understanding of prokaryotic insertion sequences (IS), their diversity in sequence, in organization and in mechanism, their distribution and impact on their host genome, and their relation to their eukaryotic cousins. We discuss several IS-related transposable elements (TE) which have been identified since the previous edition of . These include IS that use single-strand DNA intermediates and their related “domesticated” relations, insertion sequences with a common region (IS), and integrative conjugative elements (ICE), which use IS-related transposases (Tpases) for excision and integration. Several more specialized chapters in this volume include additional detailed information concerning a number of these topics. One of the major conclusions from this section is that the frontiers between the different types of TE are becoming less clear as more are identified. In the second part, we have provided a detailed description of the expanding variety of IS, which we have divided into families for convenience. We emphasize that there is no “quantitative” measure of the weight of each of the criteria we use to define a family. Our perception of these families continues to evolve and families emerge regularly as more IS are added. 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, p 555-590. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0030-2014
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Everyman’s Guide to Bacterial Insertion Sequences
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Citation: Siguier P, Gourbeyre E, Varani A, Ton-Hoang B, Chandler M. 2015. Everyman’s Guide to Bacterial Insertion Sequences, p 555-590. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0030-2014
/content/10.1128/9781555819217.chap26.fig26-1
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 and .
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10.1128/9781555819217/fig26-1.gif
Image of Figure 1
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 and .

Citation: Siguier P, Gourbeyre E, Varani A, Ton-Hoang B, Chandler M. 2015. Everyman’s Guide to Bacterial Insertion Sequences, p 555-590. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. 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 and .
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10.1128/9781555819217/fig26-2.gif
Image of Figure 2
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 and .

Citation: Siguier P, Gourbeyre E, Varani A, Ton-Hoang B, Chandler M. 2015. Everyman’s Guide to Bacterial Insertion Sequences, p 555-590. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0030-2014
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