1887

Chapter 32 : The Tn-family of Replicative Transposons

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in
Zoomout

The Tn-family of Replicative Transposons, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555819217/9781555819200_Chap32-1.gif /docserver/preview/fulltext/10.1128/9781555819217/9781555819200_Chap32-2.gif

Abstract:

The ampicillin-resistance transposon Tn is the archetype (“Tn” being synonymous with “Tn” or “Tn”; ( )) of a large and widespread family of transposons with representatives in nearly all bacterial phyla including proteobacteria, firmicutes, and cyanobacteria. Family members are modular platforms allowing assembly, diversification, and redistribution of an ever-growing arsenal of antimicrobial resistance genes, thereby contributing along with other mobile genetic elements, to the emergence of multi-drug resistances at a rate that challenges the development of new treatments ( ). They are also prevalent in horizontal transfer of large catabolic operons, allowing bacteria to metabolize various families of compounds, including industrial xenobiotic pollutants ( ).

Citation: Nicolas E, Lambin M, Dandoy D, Galloy C, Nguyen N, Oger C, Hallet B. 2015. The Tn-family of Replicative Transposons, p 693-726. 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.MDNA3-0060-2014

Key Concept Ranking

Mobile Genetic Elements
0.5233032
Group II Introns
0.46230504
0.5233032
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of Figure 1
Figure 1

Overview of the replicative transposition cycle of Tn-family transposons. Intermolecular transposition (curved arrow) from a donor (purple) to a target DNA molecule (blue) generates a cointegrate in which both molecules are fused together by directly repeated copies of the transposon. This step requires the transposase and the host replication machinery. The cointegrate is resolved by resolvase-mediated site-specific recombination (double arrow) between the duplicated copies of the transposon resolution site (boxed cross). Bracketed triangles are the terminal inverted repeats (IRs) of the transposon. The transposase and resolvase genes are represented by a purple and a white arrow, respectively. Small triangles show the short (usually 5-bp) direct repeats (DRs) that are generated upon insertion into the target. The red stippled circle indicates that a molecule that contains a copy of the transposon is immunized against further insertions due to target immunity. doi:10.1128/microbiolspec.MDNA3-0060-2014.f1

Citation: Nicolas E, Lambin M, Dandoy D, Galloy C, Nguyen N, Oger C, Hallet B. 2015. The Tn-family of Replicative Transposons, p 693-726. 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.MDNA3-0060-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2
Figure 2

The modular structure of Tn-family transposons and derived elements. (A) Tn-family transposons are constituted by the association of three classes of functional modules. The transposition module comprises the transposase gene (, purple arrow) and its associated ∼38-bp inverted repeats (IRs, bracketed triangles). The cointegrate resolution module is made of a gene encoding a site-specific recombinase from the serine- (green) or tyrosine- (magenta) family and their cognate recombination site (boxed cross). Resolution modules working with a tyrosine recombinase of the TnpS/OrfI subgroup (pale magenta) contain an additional gene coding for an accessory recombination protein (TnpT/OrfQ). “Long ” (pale green) refers to a resolvase gene that encodes a C-terminally extended member of the serine recombinase family. Passenger genes comprise a variety of phenotypic determinants and transposons that are specific to each element (gray arrows). (B) Autonomous transposons are characterized by a fully functional transposition module to mediate the mobility of the element . The simplest elements (ISs) are solely constituted by the minimal transposition module. Most characterized transposons have a typical unitary structure in which the transposase gene and its associated modules are flanked by the IR ends. Unitary elements can associate to form composite transposons containing a pair of full-length elements flanking a specific genomic segment; or pseudo-composite transposons carrying an autonomous element on one side and an isolated IR end on the other side. (C) Nonautonomous elements are Tn-family derivatives whose mobility requires a functional transposase to be provided in by a related transposon. Miniature Inverted-repeats Transposable Elements (MITEs) are solely constituted by a pair of IR ends flanking a short DNA segment that sometime contains a cointegrate resolution site. Mobile Insertion Cassettes (MICs) are nonautonomous unitary elements carrying one or more passenger genes between the ends. MITEs can also associate with passenger genes and isolated ends to form composite and pseudo-composite mobilized structures. See the text for details and the indicated examples. doi:10.1128/microbiolspec.MDNA3-0060-2014.f2

Citation: Nicolas E, Lambin M, Dandoy D, Galloy C, Nguyen N, Oger C, Hallet B. 2015. The Tn-family of Replicative Transposons, p 693-726. 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.MDNA3-0060-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3
Figure 3

Phylogenetic tree of the Tn-family transposase proteins. The different clusters and subgroups identified within the family are boxed with different colors as indicated. Transposons that contain a cointegrate resolution module working with a tyrosine recombinase are underlined. Transposons that encode a “long”, C-terminally extended resolvase of the serine-recombinase family are marked with an asterisk. The length of the branches is proportional to the average number of substitutions per residue. doi:10.1128/microbiolspec.MDNA3-0060-2014.f3

Citation: Nicolas E, Lambin M, Dandoy D, Galloy C, Nguyen N, Oger C, Hallet B. 2015. The Tn-family of Replicative Transposons, p 693-726. 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.MDNA3-0060-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 4
Figure 4

Phylogenetic tree of transposon-encoded and plasmid-encoded resolvases of the S-recombinase family. Transposons belonging to different subgroups are boxed with different colors as in Fig. 3 . Transposons encoding a “long”, C-terminally extended resolvase are marked by an asterisk. Plasmids are highlighted in blue with the name of the corresponding recombinase (when assigned) in brackets. “Mu-like” transposons are highlighted in magenta. The length of the branches is proportional to the average number of substitutions per residue. doi:10.1128/microbiolspec.MDNA3-0060-2014.f4

Citation: Nicolas E, Lambin M, Dandoy D, Galloy C, Nguyen N, Oger C, Hallet B. 2015. The Tn-family of Replicative Transposons, p 693-726. 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.MDNA3-0060-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 5
Figure 5

Phylogenetic tree of transposon-encoded and plasmid-encoded resolvases of the Y-recombinase family. Transposons belonging to different subgroups are boxed with different colors as in Fig. 3 . Plasmids are highlighted in blue with the name of the corresponding recombinase (when assigned) in brackets. Representative and well-characterized XerC and D recombinases are from (Ec), (Bs) and (Vc). The length of the branches is proportional to the average number of substitutions per residue. doi:10.1128/microbiolspec.MDNA3-0060-2014.f5

Citation: Nicolas E, Lambin M, Dandoy D, Galloy C, Nguyen N, Oger C, Hallet B. 2015. The Tn-family of Replicative Transposons, p 693-726. 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.MDNA3-0060-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 6
Figure 6

Cointegrate resolution modules working with a resolvase of the S-recombinase family. (A) Serine-resolvases are typically small proteins containing an N-terminal catalytic domain (CD) linked to a short helix-turn-helix (HTH) C-terminal DNA-binding domain (DBD). Resolvases of the “long” resolvase subgroup have a ∼100-amino acid extension (white cylinder) at the C-terminus. Position of important catalytic residues (248) is indicated, with the active site serine (circled) highlighted in magenta. (B) Organization of the resolution sites . Open arrows are the 12-bp resolvase binding motifs. Shaded arrows are for motifs with a poorer match to the consensus. Coordinates (in bp) of the first position of each motif are indicated above the recombination sites. Boxed triangles show the position of the putative Hbsu binding sites in the site of Tn and Tn. Organization of Tn, Tn and IS res sites is as proposed by Rowland ( ). Adapted from figure 6, p. 152 of reference ( ). doi:10.1128/microbiolspec.MDNA3-0060-2014.f6

Citation: Nicolas E, Lambin M, Dandoy D, Galloy C, Nguyen N, Oger C, Hallet B. 2015. The Tn-family of Replicative Transposons, p 693-726. 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.MDNA3-0060-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 7
Figure 7

Cointegrate resolution modules working with a resolvase of the Y-recombinase family. (A) Typical two-domain structure of a tyrosine recombinase. The catalytic domain is in the C-terminal part of the protein. Positions of the conserved catalytic residues (RKHR/Y) are indicated, with the active site tyrosine (circled) highlighted in magenta. Both the N- and C-terminal domains contain the DNA-binding determinants of the protein (DBD). (B) Organization of the transposon recombination sites. Open arrows indicate the recombinase binding motifs. Shaded arrows in the site of Tn are the putative DNA recognition motifs for the auxiliary protein TnpT. Numbers indicate the length and the spacing between each motif (in bp) in the recombination site. Brackets in the site show the extent of the functional recombination site as determined by deletion analysis ( ). doi:10.1128/microbiolspec.MDNA3-0060-2014.f7

Citation: Nicolas E, Lambin M, Dandoy D, Galloy C, Nguyen N, Oger C, Hallet B. 2015. The Tn-family of Replicative Transposons, p 693-726. 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.MDNA3-0060-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 8
Figure 8

Model for copy-in replicative transposition. The diagram illustrates the case of intermolecular movement of a transposon (double black line delineated by brackets) between a donor molecule (purple) and a target molecule (blue). (A) Transposition starts when the transposase introduces specific single-strand nicks at both 3′ ends of the element, releasing 3′ OH groups in the donor (red triangles). (B) The transposon 3′ OH ends are then used as a nucleophile to attack separate phosphodiester bonds in both target DNA strands. (C) The reaction generates a strand transfer product (often called a “Shapiro intermediate”) in which the transposon is linked to the target DNA through its 3′ ends, and to the donor DNA through its 5′ ends. The target phosphates (black dots) are usually staggered by five base pairs, which leaves 5-bp single-strand gaps at the junctions between the transposon and the target DNA in the strand transfer intermediate. (D) Replication initiates at the 3′ OH end(s) released by cleavage of the target to synthesize the complementary strands of the transposon (red line) and form the cointegrate. DNA synthesis also repairs the single-stranded gaps at the ends of the transposon generating directly repeated (DR) 5-bp target duplications that flank both copies of the element in the final cointegrate. doi:10.1128/microbiolspec.MDNA3-0060-2014.f8

Citation: Nicolas E, Lambin M, Dandoy D, Galloy C, Nguyen N, Oger C, Hallet B. 2015. The Tn-family of Replicative Transposons, p 693-726. 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.MDNA3-0060-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 9
Figure 9

The Tn-family transposase protein. (A) Structural organization of the transposase. The protein is depicted with three main domains based on limited proteolysis (vertical arrows) of the Tn transposase (987 amino acids) ( ). The N-terminal DNA-binding domain (DBD) has a predicted bipartite structure analogous to that of the two-helix-turn-helix (HTH) DNA-binding domain of CENP-B. The C-terminal catalytic domain contains the predicted RNase H fold region (shaded in blue). Vertical bars correspond to highly conserved (>90%) amino acid residues in a representative subset of 21 transposases of the family, with the 15 perfectly conserved residues highlighted in red. Residues of the DD-E catalytic triad are indicated. Characterized mutations that selectively affect target immunity (T+/I– mutations) are reported below the diagram. (B) Structural models for the CENP-B-like DNA-binding domain (left panels) and the RNase H fold catalytic core (right panels). The actual structures of the CENP-B–DNA co-complex ( ) and the HIV integrase RNase H fold ( ) are shown on the top, and the predicted models derived for the Tn transposase are shown below. Nonstructured regions are represented by dashed lines. Positions of secondary structures and other critical structural elements are indicated and highlighted in different colors (see text for details). Nonstructured regions are represented by dashed lines. In the RNase H fold, the DD-E catalytic residues are shown in a stick configuration colored in red. The predicted location of the 90-amino acid insert in the putative RNase H fold of TnpA is indicated by a rectangle. doi:10.1128/microbiolspec.MDNA3-0060-2014.f9

Citation: Nicolas E, Lambin M, Dandoy D, Galloy C, Nguyen N, Oger C, Hallet B. 2015. The Tn-family of Replicative Transposons, p 693-726. 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.MDNA3-0060-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 10
Figure 10

The Tn-family transposons ends. The 38-bp terminal inverted repeat (IR) sequences of 21 representative transposons of the Tn family are aligned, and perfectly or highly (>75%) conserved positions are boxed in red and yellow, respectively. The resulting consensus sequence is shown below the alignment, and a cartoon showing the orientation of the IR sequence (purple triangle) with respect to the inside (in) and outside (out) regions of the transposon is reported on the top. Position of the transposase 3′-end cleavage site is indicated by an arrow. Conserved regions corresponding to the external cleavage domain of the IR (Box A) and the internal transposase recognition domain (Box B) are indicated with brackets. The transposase recognition sequence is further subdivided into two conserved motifs (Box B 1 and Box B 2). doi:10.1128/microbiolspec.MDNA3-0060-2014.f10

Citation: Nicolas E, Lambin M, Dandoy D, Galloy C, Nguyen N, Oger C, Hallet B. 2015. The Tn-family of Replicative Transposons, p 693-726. 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.MDNA3-0060-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 11
Figure 11

Mechanism of cointegrate resolution by resolvases of the S-recombinase family. (A) The rotational strand exchange reaction catalyzed by S-recombinases. Representation of the recombination complex is inspired from the structure of the synapse showing the activated γδ resolvase tetramer bound to paired core sites I of ( ). The recombination sites are aligned in parallel. Blue arrows represent the 12-bp resolvase recognition motifs. The partner resolvase dimers are colored in pale and dark green with their catalytic domain (CD) lying at the inside of the synapse and their DNA-binding domain (DBD) at the outside. The four recombinase molecules have cleaved the DNA, generating double-strand breaks with phosphoseryl DNA–protein bonds at the 5′ ends (shown as yellow dots linked to red connectors) and free OH groups at the 3′ ends of the breaks (half-arrows). DNA strands are exchanged by 180° rotation of one pair of partner subunits with respect to the other around a flat hydrophobic interface within the tetramer. For the rejoining reaction, each free 3′ OH end attacks the phosphoseryl bond of the opposite DNA strand. (B) Topological selectivity in resolvase-mediated cointegrate resolution. Binding of resolvase dimers (green spheres) to sites I, II and III of the partner sites results in the formation of a synaptosome in which the two sites are inter-wrapped, trapping three negative crosses from the initial DNA substrate. This complex only readily forms if the starting sites are in a head-to-tail configuration on a supercoiled DNA molecule. Strand exchange by right-handed 180° rotation as in (A) generates a two-node catenane product. doi:10.1128/microbiolspec.MDNA3-0060-2014.f11

Citation: Nicolas E, Lambin M, Dandoy D, Galloy C, Nguyen N, Oger C, Hallet B. 2015. The Tn-family of Replicative Transposons, p 693-726. 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.MDNA3-0060-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 12
Figure 12

Mechanism of cointegrate resolution by the TnpI recombinase of Tn. (A) Ordered DNA strand exchange catalyzed by TnpI at the IR1–IR2 core site of the IRS. The TnpI tetramer bound to synapsed IR1–IR2 core sites is drawn according to the structure of the related Cre recombinase complexes (232). Only the C-terminal catalytic domain of the protein is shown for clarity. Each recombinase subunit is connected to its neighbors though a cyclic network of allosteric interactions that dictates its activation state during the consecutive steps of recombination. The recombination sites are brought together in an antiparallel configuration exposing one specific pair of DNA strands at the center of the synapse. In this configuration, the IR1-bound TnpI subunits (magenta) are activated to catalyze the first strand exchange and generate the Holliday junction (HJ) intermediate. The complex then isomerizes, which deactivates the IR1-bound TnpI subunits and activates the IR2-bound subunits (pink) for catalyzing the second strand exchange. For each strand exchange, the recombinase catalytic tyrosine (curved arrow) attacks the adjacent phosphate (yellow circle) to form a 3′ phosphotyrosyl protein–DNA bond, which is in turn attacked by the 5′ OH end (half-arrow) of the partner DNA strand. (B) Possible model for the topological organization of the TnpI/IRS recombination complex. TnpI binding to the DR1–DR2 accessory motifs of directly repeated IRSs generate a synaptic complex in which three DNA crosses are trapped. Proper antiparallel pairing of the IR1–IR2 core sites introduce a positive twist in the DNA so that strand exchange as in (A) generates a two-node catenane product. doi:10.1128/microbiolspec.MDNA3-0060-2014.f12

Citation: Nicolas E, Lambin M, Dandoy D, Galloy C, Nguyen N, Oger C, Hallet B. 2015. The Tn-family of Replicative Transposons, p 693-726. 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.MDNA3-0060-2014
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555819217.chap32
1. Partridge SR,, Hall RM . 2005. Evolution of transposons containing blaTEM genes. Antimicrob Agents Chemother 49 : 12671268.[PubMed] [CrossRef]
2. Toleman MA,, Walsh TR . 2011. Combinatorial events of insertion sequences and ICE in Gram-negative bacteria. FEMS Microbiol Rev 35 : 912935.[PubMed] [CrossRef]
3. Stokes HW,, Gillings MR . 2011. Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into Gram-negative pathogens. FEMS Microbiol Rev 35 : 790819.[PubMed] [CrossRef]
4. Nordmann P,, Dortet L,, Poirel L . 2012. Carbapenem resistance in Enterobacteriaceae: here is the storm! Trends Mol Med 18 : 263272.[PubMed] [CrossRef]
5. Nojiri H,, Shintani M,, Omori T . 2004. Divergence of mobile genetic elements involved in the distribution of xenobiotic-catabolic capacity. Appl Microbiol Biotechnol 64 : 154174.[PubMed] [CrossRef]
6. Tsuda M,, Ohtsubo H,, Yano H, . 2014. Mobile catabolic genetic elements in pseudomonads, p 83103. In Nojiri H,, Tsuda M,, Fukuda M,, Kamagata Y (ed), Biodegradative Bacteria: How Bacteria Degrade, Survive, Adapt, and Evolve. Springer, Japan. [CrossRef]
7. Grindley ND, . 2002. The movement of Tn3-like elements: transposition and cointegrate resolution, p 272302. In Craig NL,, Craigie R,, Gellert M,, Lambowitz AM (ed), Mobile DNA II. ASM Press, Washington D.C.
8. Curcio MJ,, Derbyshire KM . 2003. The outs and ins of transposition: from mu to kangaroo. Nat Rev Mol Cell Biol 4 : 865877.[PubMed] [CrossRef]
9. Hallet B,, Vanhooff V,, Cornet F, . 2004. DNA-specific Resolution Systems, p 145180. In Funnell BE,, Phillips GJ (ed), Plasmid Biology. ASM Press, Washington D.C. [CrossRef]
10. Toussaint A,, Merlin C . 2002. Mobile elements as a combination of functional modules. Plasmid 47 : 2635.[PubMed] [CrossRef]
11. Yurieva O,, Nikiforov V . 1996. Catalytic center quest: comparison of transposases belonging to the Tn3 family reveals an invariant triad of acidic amino acid residues. Biochem Mol Biol Int 38 : 1520.[PubMed]
12. Chandler M,, Mahillon J, . 2002. Insertion sequences revisited, p 305365. In Craig NL,, Craigie R,, Gellert M,, Lambowitz AM (ed), Mobile DNA II. ASM Press, Washington D.C.
13. 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 : 83128316.[PubMed] [CrossRef]
14. Dunon V,, Sniegowski K,, Bers K,, Lavigne R,, Smalla K,, Springael D . 2013. High prevalence of IncP-1 plasmids and IS1071 insertion sequences in on-farm biopurification systems and other pesticide-polluted environments. FEMS Microbiol Ecol 86 : 415431.[PubMed] [CrossRef]
15. Sabate M,, Navarro F,, Miro E,, Campoy S,, Mirelis B,, Barbe J,, Prats G . 2002. Novel complex sul1-type integron in Escherichia coli carrying bla(CTX-M-9). Antimicrob Agents Chemother 46 : 26562661.[PubMed] [CrossRef]
16. Mataseje LF,, Boyd DA,, Lefebvre B,, Bryce E,, Embree J,, Gravel D,, Katz K,, Kibsey P,, Kuhn M,, Langley J,, Mitchell R,, Roscoe D,, Simor A,, Taylor G,, Thomas E,, Turgeon N,, Mulvey MR . 2014. Complete sequences of a novel blaNDM-1-harbouring plasmid from Providencia rettgeri and an FII-type plasmid from Klebsiella pneumoniae identified in Canada. J Antimicrob Chemother 69 : 637642.[PubMed] [CrossRef]
17. Grindley ND,, Whiteson KL,, Rice PA . 2006. Mechanisms of site-specific recombination. Annu Rev Biochem 75 : 567605.[PubMed] [CrossRef]
18. Kholodii G,, Yurieva O,, Mindlin S,, Gorlenko Z,, Rybochkin V,, Nikiforov V . 2000. Tn5044, a novel Tn3 family transposon coding for temperature-sensitive mercury resistance. Res Microbiol 151 : 291302.[PubMed] [CrossRef]
19. Liu CC,, Huhne R,, Tu J,, Lorbach E,, Droge P . 1998. The resolvase encoded by Xanthomonas campestris transposable element ISXc5 constitutes a new subfamily closely related to DNA invertases. Genes Cells 3 : 221233.[PubMed] [CrossRef]
20. Mindlin S,, Kholodii G,, Gorlenko Z,, Minakhina S,, Minakhin L,, Kalyaeva E,, Kopteva A,, Petrova M,, Yurieva O,, Nikiforov V . 2001. Mercury resistance transposons of gram-negative environmental bacteria and their classification. Res Microbiol 152 : 811822.[PubMed] [CrossRef]
21. Yeo CC,, Tham JM,, Kwong SM,, Yiin S,, Poh CL . 1998. Tn5563, a transposon encoding putative mercuric ion transport proteins located on plasmid pRA2 of Pseudomonas alcaligenes . FEMS Microbiol Lett 165 : 253260.[PubMed] [CrossRef]
22. Schneider F,, Schwikardi M,, Muskhelishvili G,, Droge P . 2000. A DNA-binding domain swap converts the invertase gin into a resolvase. J Mol Biol 295 : 767775.[PubMed] [CrossRef]
23. Salvo JJ,, Grindley ND . 1988. The gamma delta resolvase bends the res site into a recombinogenic complex. EMBO J 7 : 36093616.[PubMed]
24. Salvo JJ,, Grindley ND . 1987. Helical phasing between DNA bends and the determination of bend direction. Nucleic Acids Res 15 : 97719779.[PubMed] [CrossRef]
25. Rowland SJ,, Stark WM,, Boocock MR . 2002. Sin recombinase from Staphylococcus aureus: synaptic complex architecture and transposon targeting. Mol Microbiol 44 : 607619.[PubMed] [CrossRef]
26. Petit MA,, Ehrlich D,, Janniere L . 1995. pAM beta 1 resolvase has an atypical recombination site and requires a histone-like protein HU. Mol Microbiol 18 : 271282.[PubMed] [CrossRef]
27. Canosa I,, Lopez G,, Rojo F,, Boocock MR,, Alonso JC . 2003. Synapsis and strand exchange in the resolution and DNA inversion reactions catalysed by the beta recombinase. Nucleic Acids Res 31 : 10381044.[PubMed] [CrossRef]
28. Rowland SJ,, Boocock MR,, Stark WM . 2006. DNA bending in the Sin recombination synapse: functional replacement of HU by IHF. Mol Microbiol 59 : 17301743.[PubMed] [CrossRef]
29. Rowland SJ,, Boocock MR,, Stark WM . 2005. Regulation of Sin recombinase by accessory proteins. Mol Microbiol 56 : 371382.[PubMed] [CrossRef]
30. Mouw KW,, Rowland SJ,, Gajjar MM,, Boocock MR,, Stark WM,, Rice PA . 2008. Architecture of a serine recombinase-DNA regulatory complex. Mol Cell 30 : 145155.[PubMed] [CrossRef]
31. Rice PA,, Mouw KW,, Montano SP,, Boocock MR,, Rowland SJ,, Stark WM . 2010. Orchestrating serine resolvases. Biochem Soc Trans 38 : 384387.[PubMed] [CrossRef]
32. Dodd HM,, Bennett PM . 1987. The R46 site-specific recombination system is a homologue of the Tn3 and gamma delta (Tn1000) cointegrate resolution system. J Gen Microbiol 133 : 20312039.[PubMed]
33. Radstrom P,, Skold O,, Swedberg G,, Flensburg J,, Roy PH,, Sundstrom L . 1994. Transposon Tn5090 of plasmid R751, which carries an integron, is related to Tn7, Mu, and the retroelements. J Bacteriol 176 : 32573268.[PubMed]
34. Kholodii GY,, Mindlin SZ,, Bass IA,, Yurieva OV,, Minakhina SV,, Nikiforov VG . 1995. Four genes, two ends, and a res region are involved in transposition of Tn5053: a paradigm for a novel family of transposons carrying either a mer operon or an integron. Mol Microbiol 17 : 11891200.[PubMed] [CrossRef]
35. Rowland SJ,, Dyke KG . 1989. Characterization of the staphylococcal beta-lactamase transposon Tn552. EMBO J 8 : 27612773.[PubMed]
36. Mahillon J,, Lereclus D . 1988. Structural and functional analysis of Tn4430: identification of an integrase-like protein involved in the co-integrate-resolution process. EMBO J 7 : 15151526.[PubMed]
37. Baum JA . 1994. Tn5401, a new class II transposable element from Bacillus thuringiensis . J Bacteriol 176 : 28352845.[PubMed]
38. Barre F-X,, Sherratt DJ, . 2002. Xer site-specific recombination: promoting chromosome segregation, p 149161. In Craig NL,, Craigie R,, Gellert M,, Lambowitz AM (ed), Mobile DNA II. ASM Press, Washington D.C.
39. Colloms SD . 2013. The topology of plasmid-monomerizing Xer site-specific recombination. Biochem Soc Trans 41 : 589594.[PubMed] [CrossRef]
40. Das B,, Martinez E,, Midonet C,, Barre FX . 2013. Integrative mobile elements exploiting Xer recombination. Trends Microbiol 21 : 2330.[PubMed] [CrossRef]
41. Genka H,, Nagata Y,, Tsuda M . 2002. Site-specific recombination system encoded by toluene catabolic transposon Tn4651. J Bacteriol 184 : 47574766.[PubMed] [CrossRef]
42. Kholodii GY,, Yurieva OV,, Gorlenko Z,, Mindlin SZ,, Bass IA,, Lomovskaya OL,, Kopteva AV,, Nikiforov VG . 1997. Tn5041: a chimeric mercury resistance transposon closely related to the toluene degradative transposon Tn4651. Microbiology 143(Pt 8): 25492556.[PubMed] [CrossRef]
43. Kholodii G,, Gorlenko Z,, Mindlin S,, Hobman J,, Nikiforov V . 2002. Tn5041-like transposons: molecular diversity, evolutionary relationships and distribution of distinct variants in environmental bacteria. Microbiology 148 : 35693582.[PubMed]
44. Yano H,, Genka H,, Ohtsubo Y,, Nagata Y,, Top EM,, Tsuda M . 2013. Cointegrate-resolution of toluene-catabolic transposon Tn4651: determination of crossover site and the segment required for full resolution activity. Plasmid 69 : 2435.[PubMed] [CrossRef]
45. Siemieniak DR,, Slightom JL,, Chung ST . 1990. Nucleotide sequence of Streptomyces fradiae transposable element Tn4556: a class-II transposon related to Tn3. Gene 86 : 19.[CrossRef]
46. Sota M,, Yano H,, Ono A,, Miyazaki R,, Ishii H,, Genka H,, Top EM,, Tsuda M . 2006. Genomic and functional analysis of the IncP-9 naphthalene-catabolic plasmid NAH7 and its transposon Tn4655 suggests catabolic gene spread by a tyrosine recombinase. J Bacteriol 188 : 40574067.[PubMed] [CrossRef]
47. Vanhooff V,, Galloy C,, Agaisse H,, Lereclus D,, Revet B,, Hallet B . 2006. Self-control in DNA site-specific recombination mediated by the tyrosine recombinase TnpI. Mol Microbiol 60 : 617629.[PubMed] [CrossRef]
48. Baum JA . 1995. TnpI recombinase: identification of sites within Tn5401 required for TnpI binding and site-specific recombination. J Bacteriol 177 : 40364042.[PubMed]
49. Clark AJ,, Warren GJ . 1979. Conjugal transmission of plasmids. Annu Rev Genet 13 : 99125.[PubMed] [CrossRef]
50. Guyer MS . 1978. The gamma delta sequence of F is an insertion sequence. J Mol Biol 126 : 347365.[PubMed] [CrossRef]
51. Palchaudhuri S,, Maas WK . 1976. Fusion of two F-prime factors in Escherichia coli studied by electron microscope heteroduplex analysis. Mol Gen Genet 146 : 215231.[PubMed] [CrossRef]
52. Green BD,, Battisti L,, Thorne CB . 1989. Involvement of Tn4430 in transfer of Bacillus anthracis plasmids mediated by Bacillus thuringiensis plasmid pXO12. J Bacteriol 171 : 104113.[PubMed]
53. Mahillon J,, Rezsohazy R,, Hallet B,, Delcour J . 1994. IS231 and other Bacillus thuringiensis transposable elements: a review. Genetica 93 : 1326.[PubMed] [CrossRef]
54. Mikosa M,, Sochacka-Pietal M,, Baj J,, Bartosik D . 2006. Identification of a transposable genomic island of Paracoccus pantotrophus DSM 11072 by its transposition to a novel entrapment vector pMMB2. Microbiology 152 : 10631073.[PubMed] [CrossRef]
55. Dziewit L,, Baj J,, Szuplewska M,, Maj A,, Tabin M,, Czyzkowska A,, Skrzypczyk G,, Adamczuk M,, Sitarek T,, Stawinski P,, Tudek A,, Wanasz K,, Wardal E,, Piechucka E,, Bartosik D . 2012. Insights into the transposable mobilome of Paracoccus spp. (Alphaproteobacteria). PLoS One 7 : e32277. [PubMed] [CrossRef]
56. Shaw JH,, Clewell DB . 1985. Complete nucleotide sequence of macrolide-lincosamide-streptogramin B-resistance transposon Tn917 in Streptococcus faecalis . J Bacteriol 164 : 782796.[PubMed]
57. Chiou CS,, Jones AL . 1993. Nucleotide sequence analysis of a transposon (Tn5393) carrying streptomycin resistance genes in Erwinia amylovora and other gram-negative bacteria. J Bacteriol 175 : 732740.[PubMed]
58. Allmeier H,, Cresnar B,, Greck M,, Schmitt R . 1992. Complete nucleotide sequence of Tn1721: gene organization and a novel gene product with features of a chemotaxis protein. Gene 111 : 1120.[CrossRef]
59. Arthur M,, Molinas C,, Depardieu F,, Courvalin P . 1993. Characterization of Tn1546, a Tn3-related transposon conferring glycopeptide resistance by synthesis of depsipeptide peptidoglycan precursors in Enterococcus faecium BM4147. J Bacteriol 175 : 117127.[PubMed]
60. Mindlin S,, Minakhin L,, Petrova M,, Kholodii G,, Minakhina S,, Gorlenko Z,, Nikiforov V . 2005. Present-day mercury resistance transposons are common in bacteria preserved in permafrost grounds since the Upper Pleistocene. Res Microbiol 156 : 9941004.[PubMed] [CrossRef]
61. Mindlin S,, Petrova M, . 2013. Mercury resistance transposons, p 3352. In Roberts AP,, Mullany P (ed), Bacterial Integrative Genetic Elements. Landes Bioscience.
62. Canton R,, Coque TM . 2006. The CTX-M beta-lactamase pandemic. Curr Opin Microbiol 9 : 466475.[PubMed] [CrossRef]
63. Van der Auwera G,, Mahillon J . 2005. TnXO1, a germination-associated class II transposon from Bacillus anthracis . Plasmid 53 : 251257.[PubMed] [CrossRef]
64. Okinaka RT,, Cloud K,, Hampton O,, Hoffmaster AR,, Hill KK,, Keim P,, Koehler TM,, Lamke G,, Kumano S,, Mahillon J,, Manter D,, Martinez Y,, Ricke D,, Svensson R,, Jackson PJ . 1999. Sequence and organization of pXO1, the large Bacillus anthracis plasmid harboring the anthrax toxin genes. J Bacteriol 181 : 65096515.[PubMed]
65. Landgraf A,, Weingart H,, Tsiamis G,, Boch J . 2006. Different versions of Pseudomonas syringae pv. tomato DC3000 exist due to the activity of an effector transposon. Mol Plant Pathol 7 : 355364.[PubMed] [CrossRef]
66. Schluter A,, Heuer H,, Szczepanowski R,, Poler SM,, Schneiker S,, Puhler A,, Top EM . 2005. Plasmid pB8 is closely related to the prototype IncP-1beta plasmid R751 but transfers poorly to Escherichia coli and carries a new transposon encoding a small multidrug resistance efflux protein. Plasmid 54 : 135148.[PubMed] [CrossRef]
67. Szuplewska M,, Ludwiczak M,, Lyzwa K,, Czarnecki J,, Bartosik D . 2014. Mobility and generation of mosaic non-autonomous transposons by Tn3-derived inverted-repeat miniature elements (TIMEs). PLoS One 9 : e105010. [PubMed] [CrossRef]
68. Naas T,, Cuzon G,, Villegas MV,, Lartigue MF,, Quinn JP,, Nordmann P . 2008. Genetic structures at the origin of acquisition of the beta-lactamase bla KPC gene. Antimicrob Agents Chemother 52 : 12571263.[PubMed] [CrossRef]
69. Cuzon G,, Naas T,, Nordmann P . 2011. Functional characterization of Tn4401, a Tn3-based transposon involved in blaKPC gene mobilization. Antimicrob Agents Chemother 55 : 53705373.[PubMed] [CrossRef]
70. Naas T,, Cuzon G,, Truong HV,, Nordmann P . 2012. Role of ISKpn7 and deletions in blaKPC gene expression. Antimicrob Agents Chemother 56 : 47534759.[PubMed] [CrossRef]
71. Grinsted J,, de la Cruz F,, Schmitt R . 1990. The Tn21 subgroup of bacterial transposable elements. Plasmid 24 : 163189.[PubMed] [CrossRef]
72. Avila P,, Grinsted J,, de la Cruz F . 1988. Analysis of the variable endpoints generated by one-ended transposition of Tn21. J Bacteriol 170 : 13501353.[PubMed]
73. Heritage J,, Bennett PM . 1985. Plasmid fusions mediated by one end of TnA. J Gen Microbiol 131 : 11301140.[PubMed]
74. Motsch S,, Schmitt R,, Avila P,, de la Cruz F,, Ward E,, Grinsted J . 1985. Junction sequences generated by ‘one-ended transposition’. Nucleic Acids Res 13 : 33353342.[PubMed] [CrossRef]
75. Motsch S,, Schmitt R . 1984. Replicon fusion mediated by a single-ended derivative of transposon Tn1721. Mol Gen Genet 195 : 281287.[PubMed] [CrossRef]
76. Revilla C,, Garcillan-Barcia MP,, Fernandez-Lopez R,, Thomson NR,, Sanders M,, Cheung M,, Thomas CM,, de la Cruz F . 2008. Different pathways to acquiring resistance genes illustrated by the recent evolution of IncW plasmids. Antimicrob Agents Chemother 52 : 14721480.[PubMed] [CrossRef]
77. Sota M,, Endo M,, Nitta K,, Kawasaki H,, Tsuda M . 2002. Characterization of a class II defective transposon carrying two haloacetate dehalogenase genes from Delftia acidovorans plasmid pUO1. Appl Environ Microbiol 68 : 23072315.[PubMed] [CrossRef]
78. Yano H,, Garruto CE,, Sota M,, Ohtsubo Y,, Nagata Y,, Zylstra GJ,, Williams PA,, Tsuda M . 2007. Complete sequence determination combined with analysis of transposition/site-specific recombination events to explain genetic organization of IncP-7 TOL plasmid pWW53 and related mobile genetic elements. J Mol Biol 369 : 1126.[PubMed] [CrossRef]
79. Yano H,, Miyakoshi M,, Ohshima K,, Tabata M,, Nagata Y,, Hattori M,, Tsuda M . 2010. Complete nucleotide sequence of TOL plasmid pDK1 provides evidence for evolutionary history of IncP-7 catabolic plasmids. J Bacteriol 192 : 43374347.[PubMed] [CrossRef]
80. Cornelis G,, Sommer H,, Saedler H . 1981. Transposon Tn951 (TnLac) is defective and related to Tn3. Mol Gen Genet 184 : 241248.[PubMed]
81. Petrovski S,, Stanisich VA . 2011. Embedded elements in the IncPbeta plasmids R772 and R906 can be mobilized and can serve as a source of diverse and novel elements. Microbiology 157 : 17141725.[PubMed] [CrossRef]
82. Gillings MR . 2014. Integrons: past, present, and future. Microbiol Mol Biol Rev 78 : 257277.[PubMed] [CrossRef]
83. Mazel D . 2006. Integrons: agents of bacterial evolution. Nat Rev Microbiol 4 : 608620.[PubMed] [CrossRef]
84. Boucher Y,, Labbate M,, Koenig JE,, Stokes HW . 2007. Integrons: mobilizable platforms that promote genetic diversity in bacteria. Trends Microbiol 15 : 301309.[PubMed] [CrossRef]
85. Partridge SR . 2011. Analysis of antibiotic resistance regions in Gram-negative bacteria. FEMS Microbiol Rev 35 : 820855.[PubMed] [CrossRef]
86. Liebert CA,, Hall RM,, Summers AO . 1999. Transposon Tn21, flagship of the floating genome. Microbiol Mol Biol Rev 63 : 507522.[PubMed]
87. Partridge SR,, Tsafnat G,, Coiera E,, Iredell JR . 2009. Gene cassettes and cassette arrays in mobile resistance integrons. FEMS Microbiol Rev 33 : 757784.[PubMed] [CrossRef]
88. Gillings MR,, Stokes HW . 2012. Are humans increasing bacterial evolvability? Trends Ecol Evol 27 : 346352.[PubMed] [CrossRef]
89. Labbate M,, Roy CP,, Stokes HW . 2008. A class 1 integron present in a human commensal has a hybrid transposition module compared to Tn402: evidence of interaction with mobile DNA from natural environments. J Bacteriol 190 : 53185327.[PubMed] [CrossRef]
90. Sajjad A,, Holley MP,, Labbate M,, Stokes HW,, Gillings MR . 2011. Preclinical class 1 integron with a complete Tn402-like transposition module. Appl Environ Microbiol 77 : 335337.[PubMed] [CrossRef]
91. Minakhina S,, Kholodii G,, Mindlin S,, Yurieva O,, Nikiforov V . 1999. Tn5053 family transposons are res site hunters sensing plasmidal res sites occupied by cognate resolvases. Mol Microbiol 33 : 10591068.[PubMed] [CrossRef]
92. Petrovski S,, Stanisich VA . 2010. Tn502 and Tn512 are res site hunters that provide evidence of resolvase-independent transposition to random sites. J Bacteriol 192 : 18651874.[PubMed] [CrossRef]
93. Kamali-Moghaddam M,, Sundstrom L . 2000. Transposon targeting determined by resolvase. FEMS Microbiol Lett 186 : 5559.[PubMed] [CrossRef]
94. Toleman MA,, Bennett PM,, Walsh TR . 2006. ISCR elements: novel gene-capturing systems of the 21st century? Microbiol Mol Biol Rev 70 : 296316.[PubMed] [CrossRef]
95. Zhao WH,, Hu ZQ . 2013. Epidemiology and genetics of CTX-M extended-spectrum beta-lactamases in Gram-negative bacteria. Crit Rev Microbiol 39 : 79101.[PubMed] [CrossRef]
96. Poirel L,, Lartigue MF,, Decousser JW,, Nordmann P . 2005. ISEcp1B-mediated transposition of blaCTX-M in Escherichia coli . Antimicrob Agents Chemother 49 : 447450.[PubMed] [CrossRef]
97. Garcillán-Barcia M,, Bernales I,, Mendiola M,, de la Cruz F, . 2002. IS91 rolling circle transposition, p 891904. In Craig NL,, Craigie R,, Gellert M,, Lambowitz AM (ed), Mobile DNA II. ASM Press, Washington D.C.
98. Poirel L,, Decousser JW,, Nordmann P . 2003. Insertion sequence ISEcp1B is involved in expression and mobilization of a bla(CTX-M) beta-lactamase gene. Antimicrob Agents Chemother 47 : 29382945.[PubMed] [CrossRef]
99. Zong Z,, Yu R,, Wang X,, Lu X . 2011. blaCTX-M-65 is carried by a Tn1722-like element on an IncN conjugative plasmid of ST131 Escherichia coli . J Med Microbiol 60 : 435441.[PubMed] [CrossRef]
100. Soler Bistue AJ,, Martin FA,, Petroni A,, Faccone D,, Galas M,, Tolmasky ME,, Zorreguieta A . 2006. Vibrio cholerae InV117, a class 1 integron harboring aac(6′)-Ib and blaCTX-M-2, is linked to transposition genes. Antimicrob Agents Chemother 50 : 19031907.[PubMed] [CrossRef]
101. Valverde A,, Canton R,, Galan JC,, Nordmann P,, Baquero F,, Coque TM . 2006. In117, an unusual In0-like class 1 integron containing CR1 and bla(CTX-M-2) and associated with a Tn21-like element. Antimicrob Agents Chemother 50 : 799802.[PubMed] [CrossRef]
102. Novais A,, Canton R,, Valverde A,, Machado E,, Galan JC,, Peixe L,, Carattoli A,, Baquero F,, Coque TM . 2006. Dissemination and persistence of blaCTX-M-9 are linked to class 1 integrons containing CR1 associated with defective transposon derivatives from Tn402 located in early antibiotic resistance plasmids of IncHI2, IncP1-alpha, and IncFI groups. Antimicrob Agents Chemother 50 : 27412750.[PubMed] [CrossRef]
103. Partridge SR,, Hall RM . 2004. Complex multiple antibiotic and mercury resistance region derived from the r-det of NR1 (R100). Antimicrob Agents Chemother 48 : 42504255.[PubMed] [CrossRef]
104. Reed RR . 1981. Resolution of cointegrates between transposons gamma delta and Tn3 defines the recombination site. Proc Natl Acad Sci USA 78 : 34283432.[PubMed] [CrossRef]
105. Kholodii G . 2001. The shuffling function of resolvases. Gene 269 : 121130.[PubMed] [CrossRef]
106. Michiels T,, Cornelis G . 1989. Site-specific recombinations between direct and inverted res sites of Tn2501. Plasmid 22 : 249255.[PubMed] [CrossRef]
107. Miller CA,, Cohen SN . 1980. F plasmid provides a function that promotes recA-independent site-specific fusions of pSC101 replicon. Nature 285 : 577579.[PubMed] [CrossRef]
108. Ishizaki K,, Ohtsubo E . 1985. Cointegration and resolution mediated by IS101 present in plasmid pSC101. Mol Gen Genet 199 : 388395.[PubMed] [CrossRef]
109. Filee J,, Siguier P,, Chandler M . 2007. Insertion sequence diversity in archaea. Microbiol Mol Biol Rev 71 : 121157.[PubMed] [CrossRef]
110. Fattash I,, Rooke R,, Wong A,, Hui C,, Luu T,, Bhardwaj P,, Yang G . 2013. Miniature inverted-repeat transposable elements: discovery, distribution, and activity. Genome 56 : 475486.[PubMed] [CrossRef]
111. Peters M,, Heinaru E,, Talpsep E,, Wand H,, Stottmeister U,, Heinaru A,, Nurk A . 1997. Acquisition of a deliberately introduced phenol degradation operon, pheBA, by different indigenous Pseudomonas species. Appl Environ Microbiol 63 : 48994906.[PubMed]
112. Siguier P,, Gourbeyre E,, Chandler M . 2014. Bacterial insertion sequences: their genomic impact and diversity. FEMS Microbiol Rev 38 : 865891.[PubMed] [CrossRef]
113. De Palmenaer D,, Siguier P,, Mahillon J . 2008. IS4 family goes genomic 1. Bmc Evolutionary Biology 8 : 18. [PubMed] [CrossRef]
114. Shapiro JA . 1979. Molecular model for the transposition and replication of bacteriophage Mu and other transposable elements. Proc Natl Acad Sci USA 76 : 19331937.[PubMed] [CrossRef]
115. Harshey RM,, Bukhari AI . 1981. A mechanism of DNA transposition. Proc Natl Acad Sci USA 78 : 10901094.[PubMed] [CrossRef]
116. Galas DJ,, Chandler M . 1981. On the molecular mechanisms of transposition. Proc Natl Acad Sci USA 78 : 48584862.[PubMed] [CrossRef]
117. Chaconas G,, Harshey RM, . 2002. Transposition of Phage Mu DNA, p 384402. In Craig NL,, Craigie R,, Gellert M,, Lambowitz AM (ed), Mobile DNA II. ASM Press, Washington D.C.
118. Mizuuchi K . 1992. Transpositional recombination: mechanistic insights from studies of mu and other elements. Annu Rev Biochem 61 : 10111051.[PubMed] [CrossRef]
119. Madison KE,, Abdelmeguid MR,, Jones-Foster EN,, Nakai H . 2012. A new role for translation initiation factor 2 in maintaining genome integrity. PLoS Genet 8 : e1002648. [PubMed] [CrossRef]
120. Lambin M,, Nicolas E,, Oger CA,, Nguyen N,, Prozzi D,, Hallet B . 2012. Separate structural and functional domains of Tn4430 transposase contribute to target immunity. Mol Microbiol 83 : 805820.[PubMed] [CrossRef]
121. Nowotny M . 2009. Retroviral integrase superfamily: the structural perspective. EMBO Rep 10 : 144151.[PubMed] [CrossRef]
122. Hickman AB,, Chandler M,, Dyda F . 2010. Integrating prokaryotes and eukaryotes: DNA transposases in light of structure. Crit Rev Biochem Mol Biol 45 : 5069.[PubMed] [CrossRef]
123. Montano SP,, Rice PA . 2011. Moving DNA around: DNA transposition and retroviral integration. Curr Opin Struct Biol 21 : 370378.[PubMed] [CrossRef]
124. Yang W,, Lee JY,, Nowotny M . 2006. Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity. Mol Cell 22 : 513.[PubMed] [CrossRef]
125. Davies DR,, Mahnke BL,, 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 : 1190411913.[PubMed] [CrossRef]
126. Davies DR,, Goryshin IY,, Reznikoff WS,, Rayment I . 2000. Three-dimensional structure of the Tn5 synaptic complex transposition intermediate. Science 289 : 7785.[PubMed] [CrossRef]
127. 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 : 715721.[PubMed] [CrossRef]
128. Tanaka Y,, Nureki O,, Kurumizaka H,, Fukai S,, Kawaguchi S,, Ikuta M,, Iwahara J,, Okazaki T,, Yokoyama S . 2001. Crystal structure of the CENP-B protein-DNA complex: the DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA. EMBO J 20 : 66126618.[PubMed] [CrossRef]
129. Evans LR,, Brown NL . 1987. Construction of hybrid Tn501/Tn21 transposases in vivo: identification of a region of transposase conferring specificity of recognition of the 38-bp terminal inverted repeats. EMBO J 6 : 28492853.[PubMed]
130. Maekawa T,, Amemura-Maekawa J,, Ohtsubo E . 1993. DNA binding domains in Tn3 transposase. Mol Gen Genet 236 : 267274.[PubMed] [CrossRef]
131. Richardson JM,, Colloms SD,, Finnegan DJ,, Walkinshaw MD . 2009. Molecular architecture of the Mos1 paired-end complex: the structural basis of DNA transposition in a eukaryote. Cell 138 : 10961108.[PubMed] [CrossRef]
132. Watkins S,, van Pouderoyen G,, Sixma TK . 2004. Structural analysis of the bipartite DNA-binding domain of Tc3 transposase bound to transposon DNA. Nucleic Acids Res 32 : 43064312.[PubMed] [CrossRef]
133. Montano SP,, Pigli YZ,, Rice PA . 2012. The mu transpososome structure sheds light on DDE recombinase evolution. Nature 491 : 413417.[PubMed] [CrossRef]
134. Casola C,, Hucks D,, Feschotte C . 2008. Convergent domestication of pogo-like transposases into centromere-binding proteins in fission yeast and mammals. Mol Biol Evol 25 : 2941.[PubMed] [CrossRef]
135. Claeys BC,, Walker N,, Liu D,, Chalmers R . 2014. Crosstalk between transposase subunits during cleavage of the mariner transposon. Nucleic Acids Res 42 : 57995808.[PubMed] [CrossRef]
136. Liu D,, Chalmers R . 2014. Hyperactive mariner transposons are created by mutations that disrupt allosterism and increase the rate of transposon end synapsis. Nucleic Acids Res 42 : 26372645.[PubMed] [CrossRef]
137. Amemura-Maekawa J,, Ohtsubo E . 1991. Functional analysis of the two domains in the terminal inverted repeat sequence required for transposition of Tn3. Gene 103 : 1116.[PubMed] [CrossRef]
138. Kans JA,, Casadaban MJ . 1989. Nucleotide sequences required for Tn3 transposition immunity. J Bacteriol 171 : 19041914.[PubMed]
139. May EW,, Grindley ND . 1995. A functional analysis of the inverted repeat of the gamma delta transposable element. J Mol Biol 247 : 578587.[PubMed] [CrossRef]
140. Nissley DV,, Lindh F,, Fennewald MA . 1991. Mutations in the inverted repeats of Tn3 affect binding of transposase and transposition immunity. J Mol Biol 218 : 335347.[PubMed] [CrossRef]
141. Wiater LA,, Grindley ND . 1991. Gamma delta transposase. Purification and analysis of its interaction with a transposon end. J Biol Chem 266 : 18411849.[PubMed]
142. Ichikawa H,, Ikeda K,, Amemura J,, Ohtsubo E . 1990. Two domains in the terminal inverted-repeat sequence of transposon Tn3. Gene 86 : 1117.[PubMed] [CrossRef]
143. New JH,, Eggleston AK,, Fennewald M . 1988. Binding of the Tn3 transposase to the inverted repeats of Tn3. J Mol Biol 201 : 589599.[PubMed] [CrossRef]
144. Ichikawa H,, Ikeda K,, Wishart WL,, Ohtsubo E . 1987. Specific binding of transposase to terminal inverted repeats of transposable element Tn3. Proc Natl Acad Sci USA 84 : 82208224.[PubMed] [CrossRef]
145. Wiater LA,, Grindley ND . 1988. Gamma delta transposase and integration host factor bind cooperatively at both ends of gamma delta. EMBO J 7 : 19071911.[PubMed]
146. Ilves H,, Horak R,, Teras R,, Kivisaar M . 2004. IHF is the limiting host factor in transposition of Pseudomonas putida transposon Tn4652 in stationary phase. Mol Microbiol 51 : 17731785.[PubMed] [CrossRef]
147. Teras R,, Jakovleva J,, Kivisaar M . 2009. Fis negatively affects binding of Tn4652 transposase by out-competing IHF from the left end of Tn4652. Microbiology 155 : 12031214.[PubMed] [CrossRef]
148. Baum JA,, Gilmer AJ,, Light Mettus AM . 1999. Multiple roles for TnpI recombinase in regulation of Tn5401 transposition in Bacillus thuringiensis . J Bacteriol 181 : 62716277.[PubMed]
149. Amemura J,, Ichikawa H,, Ohtsubo E . 1990. Tn3 transposition immunity is conferred by the transposase-binding domain in the terminal inverted-repeat sequence of Tn3. Gene 88 : 2124.[PubMed] [CrossRef]
150. Wiater LA,, Grindley ND . 1990. Uncoupling of transpositional immunity from gamma delta transposition by a mutation at the end of gamma delta. J Bacteriol 172 : 49594963.[PubMed]
151. Schumacher S,, Clubb RT,, Cai M,, Mizuuchi K,, Clore GM,, Gronenborn AM . 1997. Solution structure of the Mu end DNA-binding ibeta subdomain of phage Mu transposase: modular DNA recognition by two tethered domains. EMBO J 16 : 75327541.[PubMed] [CrossRef]
152. Sota M,, Yano H,, Nagata Y,, Ohtsubo Y,, Genka H,, Anbutsu H,, Kawasaki H,, Tsuda M . 2006. Functional analysis of unique class II insertion sequence IS1071. Appl Environ Microbiol 72 : 291297.[PubMed] [CrossRef]
153. Dillon SC,, Dorman CJ . 2010. Bacterial nucleoid-associated proteins, nucleoid structure and gene expression. Nat Rev Microbiol 8 : 185195.[PubMed] [CrossRef]
154. Browning DF,, Grainger DC,, Busby SJ . 2010. Effects of nucleoid-associated proteins on bacterial chromosome structure and gene expression. Curr Opin Microbiol 13 : 773780.[PubMed] [CrossRef]
155. Wiater LA,, Grindley ND . 1990. Integration host factor increases the transpositional immunity conferred by gamma delta ends. J Bacteriol 172 : 49514958.[PubMed]
156. Horak R,, Kivisaar M . 1998. Expression of the transposase gene tnpA of Tn4652 is positively affected by integration host factor. J Bacteriol 180 : 28222829.[PubMed]
157. Ilves H,, Horak R,, Kivisaar M . 2001. Involvement of sigma(S) in starvation-induced transposition of Pseudomonas putida transposon Tn4652. J Bacteriol 183 : 54455448.[PubMed] [CrossRef]
158. Horak R,, Ilves H,, Pruunsild P,, Kuljus M,, Kivisaar M . 2004. The ColR-ColS two-component signal transduction system is involved in regulation of Tn4652 transposition in Pseudomonas putida under starvation conditions. Mol Microbiol 54 : 795807.[PubMed] [CrossRef]
159. Horak R,, Kivisaar M . 1999. Regulation of the transposase of Tn4652 by the transposon-encoded protein TnpC. J Bacteriol 181 : 63126318.[PubMed]
160. Craig NL . 1997. Target site selection in transposition. Annu Rev Biochem 66 : 437474.[PubMed] [CrossRef]
161. Grinsted J,, Bennett PM,, Higginson S,, Richmond MH . 1978. Regional preference of insertion of Tn501 and Tn802 into RP1 and its derivatives. Mol Gen Genet 166 : 313320.[PubMed]
162. Tu CP,, Cohen SN . 1980. Translocation specificity of the Tn3 element: characterization of sites of multiple insertions. Cell 19 : 151160.[PubMed] [CrossRef]
163. Heffron F, . 1983. Tn3 and its relatives, p 223260. In Shapiro JA (ed), Mobile Genetic Elements. Academic Press Inc., New York. [CrossRef]
164. Liu L,, Whalen W,, Das A,, Berg CM . 1987. Rapid sequencing of cloned DNA using a transposon for bidirectional priming: sequence of the Escherichia coli K-12 avtA gene. Nucleic Acids Res 15 : 94619469.[PubMed] [CrossRef]
165. Davies CJ,, Hutchison CA III . 1995. Insertion site specificity of the transposon Tn3. Nucleic Acids Res 23 : 507514.[PubMed] [CrossRef]
166. Seringhaus M,, Kumar A,, Hartigan J,, Snyder M,, Gerstein M . 2006. Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae . Nucleic Acids Res 34 : e57. [PubMed] [CrossRef]
167. Kumar A,, Seringhaus M,, Biery MC,, Sarnovsky RJ,, Umansky L,, Piccirillo S,, Heidtman M,, Cheung KH,, Dobry CJ,, Gerstein MB,, Craig NL,, Snyder M . 2004. Large-scale mutagenesis of the yeast genome using a Tn7-derived multipurpose transposon. Genome Res 14 : 19751986.[PubMed] [CrossRef]
168. Kivistik PA,, Kivisaar M,, Horak R . 2007. Target site selection of Pseudomonas putida transposon Tn4652. J Bacteriol 189 : 39183921.[PubMed] [CrossRef]
169. Hallet B,, Rezsohazy R,, Mahillon J,, Delcour J . 1994. IS231A insertion specificity: consensus sequence and DNA bending at the target site. Mol Microbiol 14 : 131139.[PubMed] [CrossRef]
170. Pribil PA,, Haniford DB . 2003. Target DNA bending is an important specificity determinant in target site selection in Tn10 transposition. J Mol Biol 330 : 247259.[CrossRef]
171. Liu G,, Geurts AM,, Yae K,, Srinivasan AR,, Fahrenkrug SC,, Largaespada DS,, Takeda J,, Horie K,, Olson WK,, Hackett PB . 2005. Target-site preferences of Sleeping Beauty transposons. J Mol Biol 346 : 161173.[PubMed] [CrossRef]
172. 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 : 72807289.[PubMed] [CrossRef]
173. Nicolas E,, Lambin M,, Hallet B . 2010. Target immunity of the Tn3-family transposon Tn4430 requires specific interactions between the transposase and the terminal inverted repeats of the transposon. J Bacteriol 192 : 42334238.[PubMed] [CrossRef]
174. Sota M,, Tsuda M,, Yano H,, Suzuki H,, Forney LJ,, Top EM . 2007. Region-specific insertion of transposons in combination with selection for high plasmid transferability and stability accounts for the structural similarity of IncP-1 plasmids. J Bacteriol 189 : 30913098.[PubMed] [CrossRef]
175. 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 : 197206.[PubMed] [CrossRef]
176. 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 : 76237627.[PubMed] [CrossRef]
177. Rudolph CJ,, Upton AL,, Stockum A,, Nieduszynski CA,, Lloyd RG . 2013. Avoiding chromosome pathology when replication forks collide. Nature 500 : 608611.[PubMed] [CrossRef]
178. Wolkow CA,, Deboy RT,, Craig NL . 1996. Conjugating plasmids are preferred targets for Tn7. Genes Dev 10 : 21452157.[PubMed] [CrossRef]
179. Peters JE,, Craig NL . 2000. Tn7 transposes proximal to DNA double-strand breaks and into regions where chromosomal DNA replication terminates. Mol Cell 6 : 573582.[PubMed] [CrossRef]
180. Peters JE,, Craig NL . 2001. Tn7 recognizes transposition target structures associated with DNA replication using the DNA-binding protein TnsE. Genes Dev 15 : 737747.[PubMed] [CrossRef]
181. Hu WY,, Derbyshire KM . 1998. Target choice and orientation preference of the insertion sequence IS903. J Bacteriol 180 : 30393048.[PubMed]
182. 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 : 10551067.[PubMed] [CrossRef]
183. Ton-Hoang B,,