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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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References

/content/book/10.1128/9781555819217.chap26
1. Fiandt M,, Szybalski W,, Malamy MH . 1972. Polar mutations in lac, gal and phage lambda consist of a few IS- DNA sequences inserted with either orientation. Mol Gen Genet 119 : 223– 231.[PubMed] [CrossRef]
2. Hirsch HJ,, Saedler H,, Starlinger P . 1972. Insertion mutations in the control region of the galactose operon of E. coli. II. Physical characterization of the mutations. Mol Gen Genet 115 : 266– 276.[PubMed] [CrossRef]
3. Hirsch HJ,, Starlinger P,, Brachet P . 1972. Two kinds of insertions in bacterial genes. Mol Gen Genet 119 : 191– 206.[PubMed] [CrossRef]
4. Saedler H,, Heiss B . 1973. Multiple copies of the insertion-DNA sequences IS1 and IS2 in the chromosome of E. coli K-12. Mol Gen Genet 122 : 267– 277.[PubMed] [CrossRef]
5. Reif HJ,, Saedler H . 1974. IS1 is Involved in Deletion Formation in the gal Region of E. coli K12. Mol Gen Genet 137 : 17– 28.[PubMed]
6. Saedler H,, Reif HJ,, Hu S,, Davidson N . 1974. IS2, a genetic element for turn-off and turn-on of gene activity in E. coli . Mol Gen Genet 132 : 265– 289.[PubMed] [CrossRef]
7. Hu S,, Ohtsubo E,, Davidson N . 1975. Electron microscopic heteroduplex studies of sequence relations among plasmids of Escherichia coli: structure of F13 and related F-primes. J Bacteriol 122 : 749– 763.[PubMed]
8. Barth PT,, Datta N,, Hedges RW,, Grinter NJ . 1976. Transposition of a deoxyribonucleic acid sequence encoding trimethoprim and streptomycin resistances from R483 to other replicons. J Bacteriol 125 : 800– 810.[PubMed]
9. Hedges RW,, Jacob AE . 1974. Transposition of ampicillin resistance from RP4 to other replicons. Mol Gen Genet 132 : 31– 40.[PubMed] [CrossRef]
10. Heffron F,, Sublett R,, Hedges RW,, Jacob A,, Falkow S . 1975. Origin of the TEM-beta-lactamase gene found on plasmids. J Bacteriol 122 : 250– 256.[PubMed]
11. Arber W,, Iida S,, Jutte H,, Caspers P,, Meyer J,, Hanni C . 1979. Rearrangements of genetic material in Escherichia coli as observed on the bacteriophage P1 plasmid. Cold Spring Harb Symp Quant Biol 43( Pt 2) : 1197– 1208.[PubMed] [CrossRef]
12. So M,, Heffron F,, McCarthy BJ . 1979. The E. coli gene encoding heat stable toxin is a bacterial transposon flanked by inverted repeats of IS1. Nature 277 : 453– 456.[PubMed] [CrossRef]
13. Nevers P,, Saedler H . 1977. Transposable genetic elements as agents of gene instability and chromosomal rearrangements. Nature 268 : 109– 115.[PubMed] [CrossRef]
14. McClintock B . 1956. Controlling elements and the gene. Cold Spring Harb Symp Quant Biol 21 : 197– 216.[PubMed] [CrossRef]
15. Nyman K,, Nakamura K,, Ohtsubo H,, Ohtsubo E . 1981. Distribution of the insertion sequence IS1 in gram-negative bacteria. Nature 289 : 609– 612.[PubMed] [CrossRef]
16. Ohtsubo H,, Nyman K,, Doroszkiewicz W,, Ohtsubo E . 1981. Multiple copies of iso-insertion sequences of IS1 in Shigella dysenteriae chromosome. Nature 292 : 640– 643.[PubMed] [CrossRef]
17. Aziz RK,, Breitbart M,, Edwards RA . 2010. Transposases are the most abundant, most ubiquitous genes in nature. Nucleic Acids Res 38 : 4207– 4217.[PubMed] [CrossRef]
18. Berg DE,, Howe MM . 1989. Mobile DNA. American Society for Microbiology, Washington DC.
19. Craig NL,, Craigie R,, Gellert M,, Lambowitz A . 2002. Mobile DNA II. American Society of Microbiology, Washington DC. [CrossRef]
20. Siguier P,, Gourbeyre E,, Chandler M . 2014. Bacterial insertion sequences: their genomic impact and diversity. FEMS Microbiol Rev 38 : 865– 891.[PubMed] [CrossRef]
21. Sharma V,, Firth AE,, Antonov I,, Fayet O,, Atkins JF,, Borodovsky M,, Baranov PV . 2011. A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment. Mol Biol Evol 28 : 3195– 3211.[PubMed] [CrossRef]
22. Siguier P,, Perochon J,, Lestrade L,, Mahillon J,, Chandler M . 2006. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 34 : D32– D36.[PubMed] [CrossRef]
23. Campbell A,, Berg DE,, Botstein D,, Lederberg EM,, Novick RP,, Starlinger P,, Szybalski W . 1979. Nomenclature of transposable elements in prokaryotes. Gene 5 : 197– 206.[PubMed] [CrossRef]
24. Mahillon J,, Chandler M . 2000. Insertion sequence nomenclature. ASM News 66 : 324.
25. Galas DJ,, Chandler M, . 1989. Bacterial insertion sequences, p 109– 162. In Berg D,, Howe M (ed), Mobile DNA. American Society for Microbiology, Washington DC.
26. Chandler M,, Mahillon J, . 2002. Insertion sequences revisited, p 305– 366. In Craig NL,, Craigie R,, Gellert M,, Lambowitz A (ed), Mobile DNA, vol II. ASM Press, Washington DC. [CrossRef]
27. Mizuuchi K,, Baker TA, . 2002. Chemical mechanisms for mobilizing DNA, p 12– 23. In Craig NL,, Craigie R,, Gellert M,, Lambowitz A (ed), Mobile DNA, vol II. ASM press, Washington DC. [CrossRef]
28. Fayet O,, Ramond P,, Polard P,, Prere MF,, Chandler M . 1990. Functional similarities between retroviruses and the IS3 family of bacterial insertion sequences? Mol Microbiol 4 : 1771– 1777.[PubMed] [CrossRef]
29. Kulkosky J,, Jones KS,, Katz RA,, Mack JP,, Skalka AM . 1992. Residues critical for retroviral integrative recombination in a region that is highly conserved among retroviral/retrotransposon integrases and bacterial insertion sequence transposases. Mol Cell Biol 12 : 2331– 2338.[PubMed]
30. Khan E,, Mack JP,, Katz RA,, Kulkosky J,, Skalka AM . 1991. Retroviral integrase domains: DNA binding and the recognition of LTR sequences [published erratum appears in Nucleic Acids Res 1991 Mar 25;19(6):1358]. Nucleic Acids Res 19 : 851– 860.[PubMed] [CrossRef]
31. Hickman AB,, Chandler M,, Dyda F . 2010. Integrating prokaryotes and eukaryotes: DNA transposases in light of structure. Crit Rev Biochem Mol Biol 45 : 50– 69.[PubMed] [CrossRef]
32. Davies DR,, Braam LM,, Reznikoff WS,, Rayment I . 1999. The three-dimensional structure of a Tn5 transposase-related protein determined to 2.9-A resolution. J Biol Chem 274 : 11904– 11913.[PubMed] [CrossRef]
33. Hickman AB,, Perez ZN,, Zhou L,, Musingarimi P,, Ghirlando R,, Hinshaw JE,, Craig NL,, Dyda F . 2005. Molecular architecture of a eukaryotic DNA transposase. Nat Struct Mol Biol 12 : 715– 721.[PubMed] [CrossRef]
34. Curcio MJ,, Derbyshire KM . 2003. The outs and ins of transposition: from Mu to Kangaroo. Nat Rev Mol Cell Biol 4 : 865– 877.[PubMed] [CrossRef]
35. Turlan C,, Chandler M . 2000. Playing second fiddle: second-strand processing and liberation of transposable elements from donor DNA. Trends Microbiol 8 : 268– 274.[PubMed] [CrossRef]
36. Feng X,, Colloms SD . 2007. In vitro transposition of ISY100, a bacterial insertion sequence belonging to the Tc1/mariner family. Mol Microbiol 65 : 1432– 1443.[PubMed] [CrossRef]
37. Plasterk RH . 1996. The Tc1/mariner transposon family. Curr Top Microbiol Immunol 204 : 125– 143.[PubMed] [CrossRef]
38. Zhou L,, Mitra R,, Atkinson PW,, Burgess Hickman A,, Dyda F,, Craig NL . 2004. Transposition of hAT elements links transposable elements and V(D)J recombination. Nature 432 : 995– 1001.[PubMed] [CrossRef]
39. Choi S,, Ohta S,, Ohtsubo E . 2003. A novel IS element, IS621, of the IS110/IS492 family transposes to a specific site in repetitive extragenic palindromic sequences in Escherichia coli . J Bacteriol 185 : 4891– 4900.[PubMed] [CrossRef]
40. Buchner JM,, Robertson AE,, Poynter DJ,, Denniston SS,, Karls AC . 2005. Piv site-specific invertase requires a DEDD motif analogous to the catalytic center of the RuvC Holliday junction resolvases. J Bacteriol 187 : 3431– 3437.[PubMed] [CrossRef]
41. Chandler M,, de la Cruz F,, Dyda F,, Hickman AB,, Moncalian G,, Ton-Hoang B . 2013. Breaking and joining single-stranded DNA: the HUH endonuclease superfamily. Nat Rev Microbiol 11 : 525– 538.[PubMed] [CrossRef]
42. Taylor KL,, Churchward G . 1997. Specific DNA cleavage mediated by the integrase of conjugative transposon Tn916. J Bacteriol 179 : 1117– 1125.[PubMed]
43. Siguier P,, Gagnevin L,, Chandler M . 2009. The new IS1595 family, its relation to IS1 and the frontier between insertion sequences and transposons. Res Microbiol 160 : 232– 241.[PubMed] [CrossRef]
44. Liebert CA,, Hall RM,, Summers AO . 1999. Transposon Tn21, Flagship of the Floating Genome. Microbiol Mol Biol Rev 63 : 507– 522.[PubMed]
45. Mazel D . 2006. Integrons: agents of bacterial evolution. Nat Rev Microbiol 4 : 608– 620.[PubMed] [CrossRef]
46. Nakatsu C,, Ng J,, Singh R,, Straus N,, Wyndham C . 1991. Chlorobenzoate catabolic transposon Tn5271 is a composite class I element with flanking class II insertion sequences. Proc Natl Acad Sci USA 88 : 8312– 8316.[PubMed] [CrossRef]
47. Burrus V,, Waldor MK . 2004. Shaping bacterial genomes with integrative and conjugative elements. Res Microbiol 155 : 376– 386.[PubMed] [CrossRef]
48. Adams V,, Lyras D,, Farrow KA,, Rood JI . 2002. The clostridial mobilisable transposons. Cell Mol Life Sci 59 : 2033– 2043.[PubMed] [CrossRef]
49. Pavlovic G,, Burrus V,, Gintz B,, Decaris B,, Guedon G . 2004. Evolution of genomic islands by deletion and tandem accretion by site-specific recombination: ICESt1-related elements from Streptococcus thermophilus . Microbiology 150 : 759– 774.[PubMed] [CrossRef]
50. Brochet M,, Da Cunha V,, Couve E,, Rusniok C,, Trieu-Cuot P,, Glaser P . 2009. Atypical association of DDE transposition with conjugation specifies a new family of mobile elements. Mol Microbiol 71 : 948– 959.[PubMed] [CrossRef]
51. Guerillot R,, Da Cunha V,, Sauvage E,, Bouchier C,, Glaser P . 2013. Modular evolution of TnGBSs, a new family of integrative and conjugative elements associating insertion sequence transposition, plasmid replication, and conjugation for their spreading. J Bacteriol 195 : 1979– 1990.[PubMed] [CrossRef]
52. Guerillot R,, Siguier P,, Gourbeyre E,, Chandler M,, Glaser P . 2014. The diversity of prokaryotic DDE transposases of the mutator superfamily, insertion specificity, and association with conjugation machineries. Genome Biol Evol 6 : 260– 272.[PubMed] [CrossRef]
53. Smyth DS,, Robinson DA . 2009. Integrative and sequence characteristics of a novel genetic element, ICE6013, in Staphylococcus aureus . J Bacteriol 191 : 5964– 5975.[PubMed] [CrossRef]
54. Diaz-Aroca E,, de la Cruz F,, Zabala JC,, Ortiz JM . 1984. Characterization of the new insertion sequence IS91 from an alpha-hemolysin plasmid of Escherichia coli . Mol Gen Genet 193 : 493– 499.[PubMed] [CrossRef]
55. Toleman MA,, Bennett PM,, Walsh TR . 2006. ISCR Elements: Novel Gene-Capturing Systems of the 21st Century? Microbiol Mol Biol Rev 70 : 296– 316.[PubMed] [CrossRef]
56. Toleman MA,, Walsh TR . 2010. ISCR elements are key players in IncA/C plasmid evolution. Antimicrob Agents Chemother 54 : 3534; author reply 3534. [PubMed] [CrossRef]
57. Feschotte C,, Zhang X,, Wessler S, . 2002. Miniature inverted repeat transposable elements and their relationship to established DNA transposons, p 1147– 1158. In Craig NL,, Craigie R,, Gellert M,, Lambowitz A (ed), Mobile DNA, vol II. ASM Press, Washington DC. [CrossRef]
58. Dyall-Smith ML,, Pfeiffer F,, Klee K,, Palm P,, Gross K,, Schuster SC,, Rampp M,, Oesterhelt D . 2011. Haloquadratum walsbyi: limited diversity in a global pond. PLoS ONE 6 : e20968. [PubMed] [CrossRef]
59. Correia FF,, Inouye S,, Inouye M . 1988. A family of small repeated elements with some transposon-like properties in the genome of Neisseria gonorrhoeae . J Biol Chem 263 : 12194– 12198.[PubMed]
60. Buisine N,, Tang CM,, Chalmers R . 2002. Transposon-like Correia elements: structure, distribution and genetic exchange between pathogenic Neisseria sp. FEBS Lett 522 : 52– 58.[PubMed] [CrossRef]
61. Oggioni MR,, Claverys JP . 1999. Repeated extragenic sequences in prokaryotic genomes: a proposal for the origin and dynamics of the RUP element in Streptococcus pneumoniae . Microbiology 145( Pt 10) : 2647– 2653.[PubMed]
62. Brugger K,, Redder P,, She Q,, Confalonieri F,, Zivanovic Y,, Garrett RA . 2002. Mobile elements in archaeal genomes. FEMS Microbiol Lett 206 : 131– 141.[PubMed] [CrossRef]
63. Filee J,, Siguier P,, Chandler M . 2007. Insertion sequence diversity in archaea. Microbiol Mol Biol Rev 71 : 121– 157.[PubMed] [CrossRef]
64. Chen Y,, Braathen P,, Léonard C,, Mahillon J . 1999. MIC231, a naturally occurring mobile insertion cassette from Bacillus cereus . Mol Microbiol 32 : 657– 668.[PubMed] [CrossRef]
65. De Palmenaer D,, Vermeiren C,, Mahillon J . 2004. IS231-MIC231 elements from Bacillus cereus sensu lato are modular. Mol Microbiol 53 : 457– 467.[PubMed] [CrossRef]
66. Demerec M,, Adelberg EA,, Clark AJ,, Hartman PE . 1966. A proposal for a uniform nomenclature in bacterial genetics. Genetics 54 : 61– 76.[PubMed]
67. Nagy Z,, Chandler M . 2004. Regulation of transposition in bacteria. Res Microbiol 155 : 387– 398.[PubMed] [CrossRef]
68. Dumesic PA,, Madhani HD . 2014. Recognizing the enemy within: licensing RNA-guided genome defense. Trends Biochem Sci 39 : 25– 34.[PubMed] [CrossRef]
69. Fedoroff NV . 2012. Transposable elements, epigenetics, and genome evolution. Science 338 : 758– 767.[PubMed] [CrossRef]
70. Bikard D,, Marraffini LA . 2013. Control of Gene Expression by CRISPR-Cas systems. F1000Prime Rep 5 : 47. [PubMed]
71. Bao W,, Jurka J . 2013. Homologues of bacterial TnpB_IS605 are widespread in diverse eukaryotic transposable elements. Mob DNA 4 : 12. [PubMed] [CrossRef]
72. Parkhill J,, Sebaihia M,, Preston A,, Murphy LD,, Thomson N,, Harris DE,, Holden MT,, Churcher CM,, Bentley SD,, Mungall KL,, Cerdeno-Tarraga AM,, Temple L,, James K,, Harris B,, Quail MA,, Achtman M,, Atkin R,, Baker S,, Basham D,, Bason N,, Cherevach I,, Chillingworth T,, Collins M,, Cronin A,, Davis P,, Doggett J,, Feltwell T,, Goble A,, Hamlin N,, Hauser H,, Holroyd S,, Jagels K,, Leather S,, Moule S,, Norberczak H,, O’Neil S,, Ormond D,, Price C,, Rabbinowitsch E,, Rutter S,, Sanders M,, Saunders D,, Seeger K,, Sharp S,, Simmonds M,, Skelton J,, Squares R,, Squares S,, Stevens K,, Unwin L , , et al . 2003. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica . Nat Genet 35 : 32– 40.[PubMed] [CrossRef]
73. Preston A,, Parkhill J,, Maskell DJ . 2004. The Bordetellae: lessons from genomics. Nat Rev Microbiol 2 : 379– 390.[PubMed] [CrossRef]
74. Touchon M,, Rocha EP . 2007. Causes of insertion sequences abundance in prokaryotic genomes. Mol Biol Evol 24 : 969– 981.[PubMed] [CrossRef]
75. Gil R,, Belda E,, Gosalbes MJ,, Delaye L,, Vallier A,, Vincent-Monegat C,, Heddi A,, Silva FJ,, Moya A,, Latorre A . 2008. Massive presence of insertion sequences in the genome of SOPE, the primary endosymbiont of the rice weevil Sitophilus oryzae . Int Microbiol 11 : 41– 48.[PubMed]
76. Plague GR,, Dunbar HE,, Tran PL,, Moran NA . 2008. Extensive proliferation of transposable elements in heritable bacterial symbionts. J Bacteriol 190 : 777– 779.[PubMed] [CrossRef]
77. Moran NA,, Plague GR . 2004. Genomic changes following host restriction in bacteria. Curr Opin Genet Dev 14 : 627– 633.[PubMed] [CrossRef]
78. Andersson JO,, Andersson SG . 1999. Insights into the evolutionary process of genome degradation. Curr Opin Genet Dev 9 : 664– 671.[PubMed] [CrossRef]
79. Lawrence JG,, Hendrix RW,, Casjens S . 2001. Where are the pseudogenes in bacterial genomes? Trends Microbiol 9 : 535– 540.[PubMed] [CrossRef]
80. Mira A,, Ochman H,, Moran NA . 2001. Deletional bias and the evolution of bacterial genomes. Trends Genet 17 : 589– 596.[PubMed] [CrossRef]
81. Cerveau N,, Leclercq S,, Leroy E,, Bouchon D,, Cordaux R . 2011. Short- and long-term evolutionary dynamics of bacterial insertion sequences: insights from Wolbachia endosymbionts. Genome Biol Evol 3 : 1175– 1186.[PubMed] [CrossRef]
82. Glansdorff N,, Charlier D,, Zafarullah M . 1981. Activation of gene expression by IS2 and IS3. Cold Spring Harb Symp Quant Biol 45( Pt 1) : 153– 156.[PubMed] [CrossRef]
83. Soki J,, Eitel Z,, Urban E,, Nagy E . 2013. Molecular analysis of the carbapenem and metronidazole resistance mechanisms of Bacteroides strains reported in a Europe-wide antibiotic resistance survey. Int J Antimicrob Agents 41 : 122– 125.[PubMed] [CrossRef]
84. Aubert D,, Naas T,, Heritier C,, Poirel L,, Nordmann P . 2006. Functional characterization of IS1999, an IS4 family element involved in mobilization and expression of beta-lactam resistance genes. J Bacteriol 188 : 6506– 6514.[PubMed] [CrossRef]
85. Kieny M-P . 2012. The evolving threat of antimicrobial resistance: options for action. World Health Organization, Geneva.
86. McKenna M . 2013. The Last Resort. Nature 499 : 394– 396.[PubMed] [CrossRef]
87. Mole B . 2013. Farming up trouble. Nature 499 : 398– 400.[PubMed] [CrossRef]
88. Simons RW,, Hoopes BC,, McClure WR,, Kleckner N . 1983. Three promoters near the termini of IS10: pIN, pOUT, and pIII. Cell 34 : 673– 682.[PubMed] [CrossRef]
89. Ton-Hoang B,, Bétermier M,, Polard P,, Chandler M . 1997. Assembly of a strong promoter following IS911 circularization and the role of circles in transposition. EMBO J 16 : 3357– 3371.[PubMed] [CrossRef]
90. Perkins-Balding D,, Duval-Valentin G,, Glasgow AC . 1999. Excision of IS492 requires flanking target sequences and results in circle formation in Pseudoalteromonas atlantica . J Bacteriol 181 : 4937– 4948.[PubMed]
91. Duval-Valentin G,, Normand C,, Khemici V,, Marty B,, Chandler M . 2001. Transient promoter formation: a new feedback mechanism for regulation of IS911 transposition. EMBO J 20 : 5802– 5811.[PubMed] [CrossRef]
92. Prentki P,, Teter B,, Chandler M,, Galas DJ . 1986. Functional promoters created by the insertion of transposable element IS1. J Mol Biol 191 : 383– 393.[PubMed] [CrossRef]
93. Depardieu F,, Podglajen I,, Leclercq R,, Collatz E,, Courvalin P . 2007. Modes and modulations of antibiotic resistance gene expression. Clin Microbiol Rev 20 : 79– 114.[PubMed] [CrossRef]
94. Guynet C,, Achard A,, Hoang BT,, Barabas O,, Hickman AB,, Dyda F,, Chandler M . 2009. Resetting the site: redirecting integration of an insertion sequence in a predictable way. Mol Cell 34 : 612– 619.[PubMed] [CrossRef]
95. Mendiola MV,, de la Cruz F . 1989. Specificity of insertion of IS91, an insertion sequence present in alpha-haemolysin plasmids of Escherichia coli . Mol Microbiol 3 : 979– 984.[PubMed] [CrossRef]
96. Galas DJ,, Calos MP,, Miller JH . 1980. Sequence analysis of Tn9 insertions in the lacZ gene. J Mol Biol 144 : 19– 41.[PubMed] [CrossRef]
97. Meyer J,, Iida S,, Arber W . 1980. Does the insertion element IS1 transpose preferentially into A+T- rich DNA segments? Mol Gen Genet 178 : 471– 473.[PubMed] [CrossRef]
98. Sengstag C,, Iida S,, Hiestand-Nauer R,, Arber W . 1986. Terminal inverted repeats of prokaryotic transposable element IS186 which can generate duplications of variable length at an identical target sequence. Gene 49 : 153– 156.[PubMed] [CrossRef]
99. Peters JE,, Craig NL . 2001. Tn7: smarter than we thought. Nat Rev Mol Cell Biol 2 : 806– 814.[PubMed] [CrossRef]
100. Ton-Hoang B,, Pasternak C,, Siguier P,, Guynet C,, Hickman AB,, Dyda F,, Sommer S,, Chandler M . 2010. Single-stranded DNA transposition is coupled to host replication. Cell 142 : 398– 408.[PubMed] [CrossRef]
101. Hu WY,, Derbyshire KM . 1998. Target choice and orientation preference of the insertion sequence IS903. J Bacteriol 180 : 3039– 3048.[PubMed]
102. Spradling AC,, Bellen HJ,, Hoskins RA . 2011. Drosophila P elements preferentially transpose to replication origins. Proc Natl Acad Sci U S A 108 : 15948– 15953.[PubMed] [CrossRef]
103. Peters JE,, Craig NL . 2000. Tn7 transposes proximal to DNA double-strand breaks and into regions where chromosomal DNA replication terminates. Mol Cell 6 : 573– 582.[PubMed] [CrossRef]
104. Shi Q,, Huguet-Tapia JC,, Peters JE . 2009. Tn917 Targets the Region Where DNA Replication Terminates in Bacillus subtilis, Highlighting a Difference in Chromosome Processing in the Firmicutes. J Bacteriol 191 : 7623– 7627.[PubMed] [CrossRef]
105. Garsin DA,, Urbach J,, Huguet-Tapia JC,, Peters JE,, Ausubel FM . 2004. Construction of an Enterococcus faecalis Tn917-mediated-gene-disruption library offers insight into Tn917 insertion patterns. J Bacteriol 186 : 7280– 7289.[PubMed] [CrossRef]
106. Slater JD,, Allen AG,, May JP,, Bolitho S,, Lindsay H,, Maskell DJ . 2003. Mutagenesis of Streptococcus equi and Streptococcus suis by transposon Tn917. Vet Microbiol 93 : 197– 206.[PubMed] [CrossRef]
107. Swingle B,, O’Carroll M,, Haniford D,, Derbyshire KM . 2004. The effect of host-encoded nucleoid proteins on transposition: H-NS influences targeting of both IS903 and Tn10. Mol Microbiol 52 : 1055– 1067.[PubMed] [CrossRef]
108. Clement J-M,, Wilde C,, Bachellier S,, Lambert P,, Hofnung M . 1999. IS1397 Is Active for Transposition into the Chromosome of Escherichia coli K-12 and Inserts Specifically into Palindromic Units of Bacterial Interspersed Mosaic Elements. J Bacteriol 181 : 6929– 6936.[PubMed]
109. Tobes R,, Pareja E . 2006. Bacterial repetitive extragenic palindromic sequences are DNA targets for Insertion Sequence elements. BMC Genomics 7 : 62. [PubMed] [CrossRef]
110. Wilde C,, Escartin F,, Kokeguchi S,, Latour-Lambert P,, Lectard A,, Clement JM . 2003. Transposases are responsible for the target specificity of IS1397 and ISKpn1 for two different types of palindromic units (PUs). Nucleic Acids Res 31 : 4345– 4353.[PubMed] [CrossRef]
111. Tetu SG,, Holmes AJ . 2008. A Family of Insertion Sequences That Impacts Integrons by Specific Targeting of Gene Cassette Recombination Sites, the IS1111-attC Group. J Bacteriol 190 : 4959– 4970.[PubMed] [CrossRef]
112. Post V,, Hall RM . 2009. Insertion sequences in the IS1111 family that target the attC recombination sites of integron-associated gene cassettes. FEMS Microbiol Lett 290 : 182– 187.[PubMed] [CrossRef]
113. Hallet B,, Rezsohazy R,, Delcour J . 1991. IS231A from Bacillus thuringiensis is functional in Escherichia coli: transposition and insertion specificity. J Bacteriol 173 : 4526– 4529.[PubMed]
114. Partridge SR,, Hall RM . 2003. The IS1111 family members IS4321 and IS5075 have subterminal inverted repeats and target the terminal inverted repeats of Tn21 family transposons. J Bacteriol 185 : 6371– 6384.[CrossRef]
115. Loot C,, Turlan C,, Chandler M . 2004. Host processing of branched DNA intermediates is involved in targeted transposition of IS911. Mol Microbiol 51 : 385– 393.[PubMed] [CrossRef]
116. Reimmann C,, Haas D . 1987. Mode of replicon fusion mediated by the duplicated insertion sequence IS21 in Escherichia coli . Genetics 115 : 619– 625.[PubMed]
117. Olasz F,, Farkas T,, Kiss J,, Arini A,, Arber W . 1997. Terminal inverted repeats of insertion sequence IS30 serve as targets for transposition. J Bacteriol 179 : 7551– 7558.[PubMed]
118. Prere MF,, Chandler M,, Fayet O . 1990. Transposition in Shigella dysenteriae: isolation and analysis of IS911, a new member of the IS3 group of insertion sequences. J Bacteriol 172 : 4090– 4099.[PubMed]
119. Parks AR,, Li Z,, Shi Q,, Owens RM,, Jin MM,, Peters JE . 2009. Transposition into replicating DNA occurs through interaction with the processivity factor. Cell 138 : 685– 695.[PubMed] [CrossRef]
120. Gomez MJ,, Diaz-Maldonado H,, Gonzalez-Tortuero E,, Lopez de Saro FJ . 2014. Chromosomal replication dynamics and interaction with the beta sliding clamp determine orientation of bacterial transposable elements. Genome Biol Evol 6 : 727– 740.[PubMed] [CrossRef]
121. Qi X,, Daily K,, Nguyen K,, Wang H,, Mayhew D,, Rigor P,, Forouzan S,, Johnston M,, Mitra RD,, Baldi P,, Sandmeyer S . 2012. Retrotransposon profiling of RNA polymerase III initiation sites. Genome Res 22 : 681– 692.[PubMed] [CrossRef]
122. Shapiro JA . 1979. Molecular model for the transposition and replication of bacteriophage Mu and other transposable elements. Proc Natl Acad Sci USA 76 : 1933– 1937.[PubMed] [CrossRef]
123. Ross DG,, Swan J,, Kleckner N . 1979. Nearly precise excision: a new type of DNA alteration associated with the translocatable element Tn10. Cell 16 : 733– 738.[PubMed] [CrossRef]
124. Ross DG,, Swan J,, Kleckner N . 1979. Physical structures of Tn10-promoted deletions and inversions: role of 1400 bp inverted repetitions. Cell 16 : 721– 731.[PubMed] [CrossRef]
125. Ohtsubo E,, Zenilman M,, Ohtsubo H . 1980. Plasmids containing insertion elements are potential transposons. Proc Natl Acad Sci U S A 77 : 750– 754.[PubMed] [CrossRef]
126. Polard P,, Seroude L,, Fayet O,, Prere MF,, Chandler M . 1994. One-ended insertion of IS911. J Bacteriol 176 : 1192– 1196.[PubMed]
127. Mahillon J,, Chandler M . 1998. Insertion sequences. Microbiol Mol Biol Rev 62 : 725– 774.[PubMed]
128. Robinson DG,, Lee MC,, Marx CJ . 2012. OASIS: an automated program for global investigation of bacterial and archaeal insertion sequences. Nucleic Acids Res 40 : e174. [PubMed] [CrossRef]
129. Wagner A,, Lewis C,, Bichsel M . 2007. A survey of bacterial insertion sequences using IScan. Nucleic Acids Res 35 : 5284– 5293.[PubMed] [CrossRef]
130. MacHattie LA,, Jackowski JB, . 1977. Physical Structure and Deletion Effects of the Chloramphenicol Resistance Element Tn9 in Phage Lambda, p 219– 228. In Bukhari AI,, Shapiro JA,, Adhya SL (ed), DNA Insertion Elements, Plasmids, and Episomes. Cold Spring Harbour Laboratory, New York.
131. Chandler M,, Silver L,, Lane D,, Caro L . 1979. Properties of an autonomous r-determinant from R100.1. Cold Spring Harb Symp Quant Biol 43( Pt 2) : 1223– 1231.[PubMed] [CrossRef]
132. Peterson BC,, Rownd RH . 1985. Recombination sites in plasmid drug resistance gene amplification. J Bacteriol 164 : 1359– 1361.[PubMed]
133. Blinkowa AL,, Walker JR . 1990. Programmed ribosomal frameshifting generates the Escherichia coli DNA polymerase III gamma subunit from within the tau subunit reading frame. Nucleic Acids Res 18 : 1725– 1729.[PubMed] [CrossRef]
134. Matsutani S . 1994. Genetic evidence for IS1 transposition regulated by InsA and the delta InsA-B’-InsB species, which is generated by translation from two alternative internal initiation sites and frameshifting. J Mol Biol 240 : 52– 65.[PubMed] [CrossRef]
135. Ton-Hoang B,, Turlan C,, Chandler M . 2004. Functional domains of the IS1 transposase: analysis in vivo and in vitro . Mol Microbiol 53 : 1529– 1543.[PubMed] [CrossRef]
136. Turlan C,, Chandler M . 1995. IS1-mediated intramolecular rearrangements: formation of excised transposon circles and replicative deletions. EMBO J 14 : 5410– 5421.[PubMed]
137. Ohta S,, Tsuchida K,, Choi S,, Sekine Y,, Shiga Y,, Ohtsubo E . 2002. Presence of a characteristic D-D-E motif in IS1 transposase. J Bacteriol 184 : 6146– 6154.[PubMed] [CrossRef]
138. Ohta S,, Yoshimura E,, Ohtsubo E . 2004. Involvement of two domains with helix-turn-helix and zinc finger motifs in the binding of IS1 transposase to terminal inverted repeats. Mol Microbiol 53 : 193– 202.[PubMed] [CrossRef]
139. Parkhill J,, Achtman M,, James KD,, Bentley SD,, Churcher C,, Klee SR,, Morelli G,, Basham D,, Brown D,, Chillingworth T,, Davies RM,, Davis P,, Devlin K,, Feltwell T,, Hamlin N,, Holroyd S,, Jagels K,, Leather S,, Moule S,, Mungall K,, Quail MA,, Rajandream MA,, Rutherford KM,, Simmonds M,, Skelton J,, Whitehead S,, Spratt BG,, Barrell BG . 2000. Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491. Nature 404 : 502– 506.[PubMed] [CrossRef]
140. Filée J,, Siguier P,, Chandler M . 2007. I am what I eat and I eat what I am: acquisition of bacterial genes by giant viruses. Trends Genet 23 : 10– 15.[PubMed] [CrossRef]
141. Achard A,, Leclercq R . 2007. Characterization of a small mobilizable transposon, MTnSag1, in Streptococcus agalactiae . J Bacteriol 189 : 4328– 4331.[PubMed] [CrossRef]
142. Feschotte C . 2004. Merlin, a new superfamily of DNA transposons identified in diverse animal genomes and related to bacterial IS1016 insertion sequences. Mol Biol Evol 21 : 1769– 1780.[PubMed] [CrossRef]
143. Rousseau P,, Normand C,, Loot C,, Turlan C,, Alazard R,, Duval-Valentin G,, Chandler M, . 2002. Transposition of IS911, p 366– 383. In Craig NL,, Craigie R,, Gellert M,, Lambowitz A (ed), Mobile DNA II. American Society of Microbiology, Washington DC. [CrossRef]
144. Bhugra B,, Dybvig K . 1993. Identification and characterization of IS1138, a transposable element from Mycoplasma pulmonis that belongs to the IS3 family. Mol Microbiol 7 : 577– 584.[PubMed] [CrossRef]
145. Smith KS,, Ingram-Smith C . 2007. Methanosaeta, the forgotten methanogen? Trends Microbiol 15 : 150– 155.[PubMed] [CrossRef]
146. Petrova M,, Shcherbatova N,, Gorlenko Z,, Mindlin S . 2013. A new subgroup of the IS3 family and properties of its representative member ISPpy1. Microbiology 159 : 1900– 1910.[PubMed] [CrossRef]
147. Duval-Valentin G,, Chandler M . 2011. Cotranslational control of DNA transposition: a window of opportunity. Mol Cell 44 : 989– 996.[PubMed] [CrossRef]
148. Feschotte C,, Pritham EJ . 2007. DNA Transposons and the Evolution of Eukaryotic Genomes. Annu Rev Genet 41 : 331– 368.[PubMed] [CrossRef]
149. Morona JK,, Guidolin A,, Morona R,, Hansman D,, Paton JC . 1994. Isolation, characterization, and nucleotide sequence of IS1202, an insertion sequence of Streptococcus pneumoniae . J Bacteriol 176 : 4437– 4443.[PubMed]
150. De Palmenaer D,, Siguier P,, Mahillon J . 2008. IS4 family goes genomic. BMC Evol Biol 8 : 18. [PubMed] [CrossRef]
151. Rezsohazy R,, Hallet B,, Delcour J,, Mahillon J . 1993. The IS4 family of insertion sequences: evidence for a conserved transposase motif. Mol Microbiol 9 : 1283– 1295.[PubMed] [CrossRef]
152. Davies DR,, Goryshin IY,, Reznikoff WS,, Rayment I . 2000. Three-dimensional structure of the Tn5 synaptic complex transposition intermediate. Science 289 : 77– 85.[PubMed] [CrossRef]
153. Mazel D,, Bernard C,, Schwarz R,, Castets AM,, Houmard J,, Tandeau de Marsac N . 1991. Characterization of two insertion sequences, IS701 and IS702, from the cyanobacterium Calothrix species PCC 7601. Mol Microbiol 5 : 2165– 2170.[PubMed] [CrossRef]
154. Vilei EM,, Nicolet J,, Frey J . 1999. IS1634, a Novel Insertion Element Creating Long, Variable-Length Direct Repeats Which Is Specific for Mycoplasma mycoides subsp. mycoides Small-Colony Type. J Bacteriol 181 : 1319– 1323.[PubMed]
155. Klenchin VA,, Czyz A,, Goryshin IY,, Gradman R,, Lovell S,, Rayment I,, Reznikoff WS . 2008. Phosphate coordination and movement of DNA in the Tn5 synaptic complex: role of the (R)YREK motif 10.1093/nar/gkn577. Nucl Acids Res 36 : 5855– 5862.[PubMed] [CrossRef]
156. Rieck B,, Tourigny DS,, Crosatti M,, Schmid R,, Kochar M,, Harrison EM,, Ou HY,, Turton JF,, Rajakumar K . 2012. Acinetobacter insertion sequence ISAba11 belongs to a novel family that encodes transposases with a signature HHEK motif. Appl Environ Microbiol 78 : 471– 480.[PubMed] [CrossRef]
157. Zhang X,, Jiang N,, Feschotte C,, Wessler SR . 2004. PIF- and Pong-like transposable elements: distribution, evolution and relationship with Tourist-like miniature inverted-repeat transposable elements. Genetics 166 : 971– 986.[PubMed] [CrossRef]
158. Berg DE,, Davies J,, Allet B,, Rochaix JD . 1975. Transposition of R factor genes to bacteriophage lambda. Proc Natl Acad Sci USA 72 : 3628– 3632.[PubMed] [CrossRef]
159. Miriagou V,, Carattoli A,, Tzelepi E,, Villa L,, Tzouvelekis LS . 2005. IS26-Associated In4-Type Integrons Forming Multiresistance Loci in Enterobacterial Plasmids. Antimicrob Agents Chemother 49 : 3541– 3543.[PubMed] [CrossRef]
160. Partridge SR,, Zong Z,, Iredell JR . 2011. Recombination in IS26 and Tn2 in the Evolution of Multiresistance Regions Carrying blaCTX-M-15 on Conjugative IncF Plasmids from Escherichia coli . Antimicrob Agents Chemother 55 : 4971– 4978.[PubMed] [CrossRef]
161. Zhu Y-G,, Johnson TA,, Su J-Q,, Qiao M,, Guo G-X,, Stedtfeld RD,, Hashsham SA,, Tiedje JM . 2013. Diverse and abundant antibiotic resistance genes in Chinese swine farms. Proc Natl Acad Sci USA 110 : 3435– 3440.[PubMed] [CrossRef]
162. Kato K,, Ohtsuki K,, Mitsuda H,, Yomo T,, Negoro S,, Urabe I . 1994. Insertion sequence IS6100 on plasmid pOAD2, which degrades nylon oligomers. J Bacteriol 176 : 1197– 1200.[PubMed]
163. Hall RM,, Brown HJ,, Brookes DE,, Stokes HW . 1994. Integrons found in different locations have identical 5′ ends but variable 3′ ends. J Bacteriol 176 : 6286– 6294.[PubMed]
164. Sundin GW,, Bender CL . 1995. Expression of the strA-strB streptomycin resistance genes in Pseudomonas syringae and Xanthomonas campestris and characterization of IS6100 in X. campestris . Appl Environ Microbiol 61 : 2891– 2897.[PubMed]
165. Simpson AE,, Skurray RA,, Firth N . 2000. An IS257-derived hybrid promoter directs transcription of a tetA(K) tetracycline resistance gene in the Staphylococcus aureus chromosomal mec region. J Bacteriol 182 : 3345– 3352.[PubMed] [CrossRef]
166. Bertini A,, Poirel L,, Bernabeu S,, Fortini D,, Villa L,, Nordmann P,, Carattoli A . 2007. Multicopy blaOXA-58 gene as a source of high-level resistance to carbapenems in Acinetobacter baumannii . Antimicrob Agents Chemother 51 : 2324– 2328.[PubMed] [CrossRef]
167. Zienkiewicz M,, Kern-Zdanowicz I,, Carattoli A,, Gniadkowski M,, Ceglowski P . 2013. Tandem multiplication of the IS26-flanked amplicon with the bla(SHV-5) gene within plasmid p1658/97. FEMS Microbiol Lett 341 : 27– 36.[PubMed] [CrossRef]
168. Loli A,, Tzouvelekis LS,, Tzelepi E,, Carattoli A,, Vatopoulos AC,, Tassios PT,, Miriagou V . 2006. Sources of diversity of carbapenem resistance levels in Klebsiella pneumoniae carrying blaVIM-1. J Antimicrob Chemother 58 : 669– 672.[PubMed] [CrossRef]
169. Doublet B,, Praud K,, Weill FX,, Cloeckaert A . 2009. Association of IS26-composite transposons and complex In4-type integrons generates novel multidrug resistance loci in Salmonella genomic island 1. J Antimicrob Chemother 63 : 282– 289.[PubMed] [CrossRef]
170. Nigro SJ,, Farrugia DN,, Paulsen IT,, Hall RM . 2013. A novel family of genomic resistance islands, AbGRI2, contributing to aminoglycoside resistance in Acinetobacter baumannii isolates belonging to global clone 2. J Antimicrob Chemother 68 : 554– 557.[PubMed] [CrossRef]
171. Cullik A,, Pfeifer Y,, Prager R,, von Baum H,, Witte W . 2010. A novel IS26 structure surrounds blaCTX-M genes in different plasmids from German clinical Escherichia coli isolates. J Med Microbiol 59 : 580– 587.[PubMed] [CrossRef]
172. Trieu-Cuot P,, Courvalin P . 1985. Transposition behavior of IS15 and its progenitor IS15-delta: are cointegrates exclusive end products? Plasmid 14 : 80– 89.[PubMed] [CrossRef]
173. Harmer CJ,, Moran RA,, Hall RM . 2014. Movement of IS26-associated antibiotic resistance genes occurs via a translocatable unit that includes a single IS26 and preferentially inserts adjacent to another IS26. MBio 5 : e01801– 01814.[PubMed] [CrossRef]
174. Riess G,, Holloway BW,, Puhler A . 1980. R68.45, a plasmid with chromosome mobilizing ability (Cma) carries a tandem duplication. Genet Res 36 : 99– 109.[PubMed] [CrossRef]
175. Willetts NS,, Crowther C,, Holloway BW . 1981. The insertion sequence IS21 of R68.45 and the molecular basis for mobilization of the bacterial chromosome. Plasmid 6 : 30– 52.[PubMed] [CrossRef]
176. Watson JM,, Holloway BW . 1978. Chromosome mapping in Pseudomonas aeruginosa PAT. J Bacteriol 133 : 1113– 1125.[PubMed]
177. Berger B,, Haas D . 2001. Transposase and cointegrase: specialized transposition proteins of the bacterial insertion sequence IS21 and related elements. Cell Mol Life Sci 58 : 403– 419.[PubMed] [CrossRef]
178. Ammendola S,, Politi L,, Scandurra R . 1998. Cloning and sequencing of ISC1041 from the archaeon Sulfolobus solfataricus MT-4, a new member of the IS30 family of insertion elements [In Process Citation]. FEBS Lett 428 : 217– 223.[PubMed] [CrossRef]
179. Dalrymple B . 1987. Novel rearrangements of IS30 carrying plasmids leading to the reactivation of gene expression. Mol Gen Genet 207 : 413– 420.[PubMed] [CrossRef]
180. Rasmussen JL,, Odelson DA,, Macrina FL . 1987. Complete nucleotide sequence of insertion element IS4351 from Bacteroides fragilis . J Bacteriol 169 : 3573– 3580.[PubMed]
181. Rudant E,, Courvalin P,, Lambert T . 1998. Characterization of IS18, an Element Capable of Activating the Silent aac(6′)-Ij Gene of Acinetobacter sp. 13 Strain BM2716 by Transposition. Antimicrob Agents Chemother 42 : 2759– 2761.[PubMed]
182. Stalder R,, Caspers P,, Olasz F,, Arber W . 1990. The N-terminal domain of the insertion sequence 30 transposase interacts specifically with the terminal inverted repeats of the element. J Biol Chem 265 : 3757– 3762.[PubMed]
183. Nagy Z,, Szabó M,, Chandler M,, Olasz F . 2004. Analysis of the N-terminal DNA binding domain of the IS30 transposase. Mol Microbiol 54 : 478– 488.[PubMed] [CrossRef]
184. Olasz F,, Stalder R,, Arber W . 1993. Formation of the tandem repeat (IS30)2 and its role in IS30- mediated transpositional DNA rearrangements. Mol Gen Genet 239 : 177– 187.[PubMed]
185. Olasz F,, Farkas T,, Stalder R,, Arber W . 1997. Mutations in the carboxy-terminal part of IS30 transposase affect the formation and dissolution of (IS30)2 dimer. FEBS Lett 413 : 453– 461.[PubMed] [CrossRef]
186. Kiss J,, Olasz F . 1999. Formation and transposition of the covalently closed IS30 circle: the relation between tandem dimers and monomeric circles. Mol Microbiol 34 : 37– 52.[PubMed] [CrossRef]
187. Kiss J,, Szabo M,, Olasz F . 2003. Site-specific recombination by the DDE family member mobile element IS30 transposase. Proc Natl Acad Sci USA 100 : 15000– 15005.[PubMed] [CrossRef]
188. Szeverenyi I,, Nagy Z,, Farkas T,, Olasz F,, Kiss J . 2003. Detection and analysis of transpositionally active head-to-tail dimers in three additional Escherichia coli IS elements. Microbiology 149 : 1297– 1310.[PubMed] [CrossRef]
189. Kiss J,, Nagy Z,, Toth G,, Kiss GB,, Jakab J,, Chandler M,, Olasz F . 2007. Transposition and target specificity of the typical IS30 family element IS1655 from Neisseria meningitidis . Mol Microbiol 63 : 1731– 1747.[PubMed] [CrossRef]
190. Szabó M,, Kiss J,, Nagy Z,, Chandler M,, Olasz F . 2008. Sub-terminal Sequences Modulating IS30 Transposition in Vivo and in Vitro . J Mol Biol 375 : 337– 352.[PubMed] [CrossRef]
191. Hwa V,, Shoemaker NB,, Salyers AA . 1988. Direct repeats flanking the Bacteroides transposon Tn4351 are insertion sequence elements. J Bacteriol 170 : 449– 451.[PubMed]
192. Brynestad S,, Granum PE . 1999. Evidence that Tn5565, which includes the enterotoxin gene in Clostridium perfringens, can have a circular form which may be a transposition intermediate. FEMS Microbiol Lett 170 : 281– 286.[PubMed] [CrossRef]
193. Machida Y,, Sakurai M,, Kiyokawa S,, Ubasawa A,, Suzuki Y,, Ikeda JE . 1984. Nucleotide sequence of the insertion sequence found in the T-DNA region of mutant Ti plasmid pTiA66 and distribution of its homologues in octopine Ti plasmid. Proc Natl Acad Sci USA 81 : 7495– 7499.[PubMed] [CrossRef]
194. Gourbeyre E,, Siguier P,, Chandler M . 2010. Route 66: investigations into the organisation and distribution of the IS66 family of prokaryotic insertion sequences. Res Microbiol 161 : 136– 143.[PubMed] [CrossRef]
195. Egelseer EM,, Idris R,, Jarosch M,, Danhorn T,, Sleytr UB,, Sara M . 2000. ISBst12, a novel type of insertion-sequence element causing loss of S- layer-gene expression in Bacillus stearothermophilus ATCC 12980. Microbiology 146( Pt 9) : 2175– 2183.[PubMed]
196. Han CG,, Shiga Y,, Tobe T,, Sasakawa C,, Ohtsubo E . 2001. Structural and functional characterization of IS679 and IS66-family elements. J Bacteriol 183 : 4296– 4304.[PubMed] [CrossRef]
197. Haren L,, Polard P,, Ton-Hoang B,, Chandler M . 1998. Multiple oligomerisation domains in the IS911 transposase: a leucine zipper motif is essential for activity. J Mol Biol 283 : 29– 41.[PubMed] [CrossRef]
198. Dordet Frisoni E,, Marenda MS,, Sagné E,, Nouvel LX,, Guérillot R,, Glaser P,, Blanchard A,, Tardy F,, Sirand-Pugnet P,, Baranowski E,, Citti C . 2013. ICEA of Mycoplasma agalactiae: a new family of self-transmissible integrative elements that confers conjugative properties to the recipient strain. Mol Microbiol 89 : 1226– 1239.[PubMed] [CrossRef]
199. Hennig S,, Ziebuhr W . 2010. Characterization of the Transposase Encoded by IS256, the Prototype of a Major Family of Bacterial Insertion Sequence Elements. J Bacteriol 192 : 4153– 4163.[PubMed] [CrossRef]
200. Yuan Y-W,, Wessler SR . 2011. The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies. Proc Natl Acad Sci USA 108 : 7884– 7889.[PubMed] [CrossRef]
201. Lyon BR,, Gillespie MT,, Skurray RA . 1987. Detection and characterization of IS256, an insertion sequence in Staphylococcus aureus . J Gen Microbiol 133 : 3031– 3038.[PubMed] [CrossRef]
202. Lyon BR,, May JW,, Skurray RA . 1984. Tn4001: a gentamicin and kanamycin resistance transposon in Staphylococcus aureus . Mol Gen Genet 193 : 554– 556.[PubMed] [CrossRef]
203. Loessner I,, Dietrich K,, Dittrich D,, Hacker J,, Ziebuhr W . 2002. Transposase-dependent formation of circular IS256 derivatives in Staphylococcus epidermidis and Staphylococcus aureus . J Bacteriol 184 : 4709– 4714.[PubMed] [CrossRef]
204. Eisen JA,, Benito MI,, Walbot V . 1994. Sequence similarity of putative transposases links the maize Mutator autonomous element and a group of bacterial insertion sequences. Nucleic Acids Res 22 : 2634– 2636.[PubMed] [CrossRef]
205. Hua-Van Al,, Capy P . 2008. Analysis of the DDE Motif in the Mutator Superfamily. J Mol Evol 67 : 670– 681.[PubMed] [CrossRef]
206. Prudhomme M,, Turlan C,, Claverys JP,, Chandler M . 2002. Diversity of Tn4001 transposition products: the flanking IS256 elements can form tandem dimers and IS circles. J Bacteriol 184 : 433– 443.[PubMed] [CrossRef]
207. Feng X,, Bednarz AL,, Colloms SD . 2010. Precise targeted integration by a chimaeric transposase zinc-finger fusion protein. Nucl Acids Res 38 : 1204– 1216.[PubMed] [CrossRef]
208. Cassier-Chauvat C,, Poncelet M,, Chauvat F . 1997. Three insertion sequences from the Cyanobacterium synechocystis PCC6803 support the occurrence of horizontal DNA transfer among bacteria. Gene 195 : 257– 266.[PubMed] [CrossRef]
209. Dawson A,, Finnegan DJ . 2003. Excision of the Drosophila mariner transposon mos1. Comparison with bacterial transposition and v(d)j recombination. Mol Cell 11 : 225– 235.[PubMed] [CrossRef]
210. Richardson JM,, Dawson A,, O’Hagan N,, Taylor P,, Finnegan DJ,, Walkinshaw MD . 2006. Mechanism of Mos1 transposition: insights from structural analysis. EMBO J