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Chapter 6 : Plasmids and Transposons

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Abstract:

This chapter describes the basic mechanisms of maintenance and transposition of the plasmids and transposons identified or known to function in the enterococci. Their use as genetic tools for studying enterococci is also discussed. Three classes of plasmids are known to be capable of replication in the enterococci: the rolling circle replicating (RCR) plasmids, the Incl8 plasmids, and the pheromone-responsive plasmids. A large number of individual transposons and several transposon classes have been described in enterococci. Enterococcal transposons generally fall into one of three classes: Tn3-family transposons, composite transposons, and conjugative transposons. The first two classes are widespread throughout the bacterial domain and their transposition mechanisms have been well described in and other gram-negative bacteria. The distribution and characteristics of several important Tn3-family and composite transposons native to the enterococci are described. Both the pheromone-responsive plasmids and the broad-hostrange plasmids have been implicated in the transfer of antibiotic resistance in the clinical setting. Work on plasmids and transposons in the enterococci and in other low G+C gram-positive bacteria has revealed that the general themes of plasmid and transposon function are conserved between gram-negative and gram-positive bacteria. Clearly, more information on plasmid biology and chromosomal genomics of diverse bacterial organisms is required before the hypothesis can be tested.

Citation: Weaver K, Rice L, Churchward G. 2002. Plasmids and Transposons, p 219-263. In Gilmore M, Clewell D, Courvalin P, Dunny G, Murray B, Rice L (ed), The Enterococci. ASM Press, Washington, DC. doi: 10.1128/9781555817923.ch6

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Genetic Elements
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Genetic Recombination
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DNA Polymerase III
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DNA Polymerase I
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Figures

Image of Figure 1
Figure 1

Model for replication of RCR plasmids. For details, see the text. The Rep protein is shown as a dimer in the model, but different initiators may function as monomers or oligomers. Similarly, the inactivated Rep protein may be released as a monomer, dimer, or oligomer. SC, supercoiled. Reprinted by permission from reference .

Citation: Weaver K, Rice L, Churchward G. 2002. Plasmids and Transposons, p 219-263. In Gilmore M, Clewell D, Courvalin P, Dunny G, Murray B, Rice L (ed), The Enterococci. ASM Press, Washington, DC. doi: 10.1128/9781555817923.ch6
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Image of Figure 2
Figure 2

General organization of Incl8 replicons. and encode protein and antisense RNA copy control functions, respectively ( for pAMl, pIP501, pSM19035; in pAMl and RNAIII in the others), encodes the replication initiator protein ( in pAMl, pIPS0l, and pSM19035, respectively), contains the sites of protein action. The black box is the origin of replication, the open box is the primosome assembly site, and the hatched box is the resolution site, encodes the multimer resolvase ( in pAMl, pIP501 and pSM19035, respectively). encodes a topoisomerase ( in pAMl and γ in pSM19035). encodes a protein with homology to ParA-type partition proteins (δ in pSM19035). The , and genes encode a postsegregational killing system. The specific functions of each of these genes is described in the text.

Citation: Weaver K, Rice L, Churchward G. 2002. Plasmids and Transposons, p 219-263. In Gilmore M, Clewell D, Courvalin P, Dunny G, Murray B, Rice L (ed), The Enterococci. ASM Press, Washington, DC. doi: 10.1128/9781555817923.ch6
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Image of Figure 3
Figure 3

Model for initiation of pAM1 replication. The RNA polymerase and the RepE protein are represented by gray and black ovals, respectively. RNA is shown as a thick line, DNA strands as thin lines. The origin (ori) and the position of initiation of leading strand synthesis (+1) are indicated. The direction of transcription is indicated by a horizontal arrow. Two models are shown. In the first model, on the left, a DNA-RNA heteroduplex forms in the origin by an unknown mechanism (step 1). An RNase H activity, which could be carried by the RepE protein or a host-encoded protein, cleaves the RNA part of the heteroduplex at several positions, including the initiation site and a position located 10 nt upstream (step 2). The 5′ part of the transcript is released and the 10-nt-long oligoribonucleotide is used as a primer by Pol I (step 3). In the second model on the right, transcription stops in the origin, because of the presence of particular sequences or the RepE protein bound to the origin, acting as roadblock for the RNA polymerase (step 4). An RNA polymerase-associated RNase activity cleaves the RNA molecule ≈10 nt upstream of the initiation site (step 5). The 5′ part of the transcript is released and the 10-nt-long oligoribonucleotide remains annealed to its template and is used as a primer by Pol I (step 6). Reprinted by permission from reference 16. For an updated model, see Fig. 11 in reference .

Citation: Weaver K, Rice L, Churchward G. 2002. Plasmids and Transposons, p 219-263. In Gilmore M, Clewell D, Courvalin P, Dunny G, Murray B, Rice L (ed), The Enterococci. ASM Press, Washington, DC. doi: 10.1128/9781555817923.ch6
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Figure 4

(A) Generalized organization of pheromone plasmid replicons. The gene ( in pCFl0) encodes the replication initiator protein, and the cross-hatched box within represents the repeat structure, which constitutes the replication origin. The size of the origin region is similar in each -related gene, but the organization and sequence of the repeats vary. The ( in pCFl0) gene is a member of the ParA family of partition proteins and the pair most likely encodes a ParAB partition pair ( in pCFl0). In all pheromone plasmids the genes are flanked by a series of identical repeats, denoted by the vertically lined boxes. These repeats probably encode the site of action of the RepBC partition proteins. The number, sequence, and organization of the repeats vary between the different pheromone plasmids. The genes of pAM373 are inverted with respect to . The locus is an antisense RNA regulated PSK system (see text). A variable number of genes apparently unrelated to replication are located between and . (B) Organization of the iterons of pheromone plasmids. Each box represents a cluster of repeats, with the number of repeats given inside the box. Distance between clusters is given below. In each case, at least one repeat overlaps the putative promoter. Sequence data are provided in the following references: 185 and 187 for pADl; 73 for pCFl0; 55 for pPD1, except for the region downstream of from 183a; 36 for pAM373. Repeat organization is as published for pADl and according to the interpretation of the author (K. E. Weaver) for the other three.

Citation: Weaver K, Rice L, Churchward G. 2002. Plasmids and Transposons, p 219-263. In Gilmore M, Clewell D, Courvalin P, Dunny G, Murray B, Rice L (ed), The Enterococci. ASM Press, Washington, DC. doi: 10.1128/9781555817923.ch6
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Figure 5

Organization of the pADl PSK locus. The boxes with arrows indicate positions of the promoters (P-RNA I and P-RNA II) for the convergently transcribed RNAs. Solid boxes indicate the regions at the 5′ end of each gene encoding complementary sequences in RNA I and RNA II. The stipled box shows the location of the bidirectional terminator used to terminate transcription of both RNAs. The terminator stem-loop represents another important complementary region required for RNA-RNA interaction. The checkerboard box designated shows the coding region and associated ribosome binding site for a 33-amino-acid open reading frame believed to encode the toxic component of the PSK system.

Citation: Weaver K, Rice L, Churchward G. 2002. Plasmids and Transposons, p 219-263. In Gilmore M, Clewell D, Courvalin P, Dunny G, Murray B, Rice L (ed), The Enterococci. ASM Press, Washington, DC. doi: 10.1128/9781555817923.ch6
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Figure 6

Prototype representation of the two families of Tn-type transposons (Tn-family, Tn-family) and a comparison of two highly prevalent enterococcal transposons: Tn, encoding VanA-type vancomycin resistance, and Tn, encoding -type macroHde-lincosamide-streptogramin B resistance. The transposons are not drawn to scale. Arrows indicate the direction of transcription of the indicated genes or operons. This figure is adapted from references , and .

Citation: Weaver K, Rice L, Churchward G. 2002. Plasmids and Transposons, p 219-263. In Gilmore M, Clewell D, Courvalin P, Dunny G, Murray B, Rice L (ed), The Enterococci. ASM Press, Washington, DC. doi: 10.1128/9781555817923.ch6
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Image of Figure 7
Figure 7

Schematic drawing of composite enterococcal transposon . Segments along the upper line represent regions most likely derived from streptococcal or enterococcal sources. Segments along the lower line are typical for staphylococcal plasmids. The segment in the middle represents a structure indistinguishable from , an aminoglycoside-resistant transposon found widely distributed in staphylococcal and streptococcal/enterococcal species. Sm, streptomycin resistance gene; Mob, region typical of mobilization regions from small staphylococcal plasmids; Erm, erythromycin ribosomal methylase within a truncated version of Tn917; Rep, replication region typical for streptococcal/enterococcal broad host-range plasmids; Mer, mercury resistance operon; Bla, -lactamase gene encoded by Tn552. The representative shapes for the various insertion sequences are indicated to the left of the diagram.

Citation: Weaver K, Rice L, Churchward G. 2002. Plasmids and Transposons, p 219-263. In Gilmore M, Clewell D, Courvalin P, Dunny G, Murray B, Rice L (ed), The Enterococci. ASM Press, Washington, DC. doi: 10.1128/9781555817923.ch6
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Image of Figure 8
Figure 8

Genetic map of . The gray line represents transposon DNA and the thick black arrows represent open reading frames. Four short reading frames, , to the right of , to the right of , to the right of ; and , to the right of are not shown. The position of the origin of conjugal DNA transfer, oriT, is indicated between and . The thin arrows indicate five promoters and their direction of transcription.

Citation: Weaver K, Rice L, Churchward G. 2002. Plasmids and Transposons, p 219-263. In Gilmore M, Clewell D, Courvalin P, Dunny G, Murray B, Rice L (ed), The Enterococci. ASM Press, Washington, DC. doi: 10.1128/9781555817923.ch6
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Image of Figure 9
Figure 9

Binding sites for Int and Xis on Tn916. The thick black line represents transposon DNA. The diamonds labeled Int-C show where the C-terminal domains of Int bind to the transposon ends and flanking bacterial DNA. The black triangles labeled DR-2 and Int-N show the positions and relative orientation of binding sites for the N-tenrtinal domain of integrase. The open triangles labeled Xis show the positions and relative orientation of binding sites for Xis.

Citation: Weaver K, Rice L, Churchward G. 2002. Plasmids and Transposons, p 219-263. In Gilmore M, Clewell D, Courvalin P, Dunny G, Murray B, Rice L (ed), The Enterococci. ASM Press, Washington, DC. doi: 10.1128/9781555817923.ch6
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Image of Figure 10
Figure 10

Model for the alignment of the left and right ends of Tn916 during excision, (adapted from reference ). The left and right parts of the figure show two different views of the complex. The heavy black line represents the DNA of the right end of Tn916 and the open line represents the DNA of the left end of Tn916. The hatched open line represents flanking bacterial DNA. The positions indicated by B, T′, B′ and T indicate binding sites for the C-terminal domain of Int. The positions indicated by Nl, N2, Nl′, and N2′ indicate binding sites for the N-terminal domain of Int. In the left part of the figure, the large circles represent the C-terminal domain of Int molecules, and the small circles represent the N-terminal domains. In the right part of the figure, the large cylinders represent the C-terminal domain of Int, and the small circles represent the N-terminal domain. The hatched circle in the left part of the figure and the hatched cylinder on the right represent an Int molecule that may be recruited into the complex from solution. The hatched object labeled Xis indicates where Xis binds at the left end of the transposon.

Citation: Weaver K, Rice L, Churchward G. 2002. Plasmids and Transposons, p 219-263. In Gilmore M, Clewell D, Courvalin P, Dunny G, Murray B, Rice L (ed), The Enterococci. ASM Press, Washington, DC. doi: 10.1128/9781555817923.ch6
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Image of Figure 11
Figure 11

Model for transposition. The thick lines represent and the thin lines represent the DNA adjacent to the transposon. Coupling sequences are indicated by the hypothetical nucleotide pairs X-Y, Q-R, and A-B. (A) Cleavage of one DNA strand at each end of the transposon on the 5′ side of the coupling sequence, indicated by the vertical arrows, followed by DNA strand exchange leads to the formation of a Holliday junction intermediate. A second round of cleavage and DNA strand exchange results in the formation of an excised circular intermediate form of the transposon that contains a heteroduplex region formed from the base pairs originally present in the coupling sequences flanking the transposon in the donor. The reciprocal product can be processed by DNA replication to yield a pair of excisant molecules, each carrying one of the coupling sequences originally flanking the transposon. (B) Following introduction of a single strand of the circular intermediate form of the transposon into the recipient, the complementary strand is synthesized to form a new intermediate with only one of the coupling sequences originally flanking the transposon in the donor. A similar recombination event to that shown in panel A results in the transposon being integrated into the recipient DNA where it is flanked on each side by a heteroduplex region composed of coupling sequence and target DNA. Following replication, two DNA molecules are produced, with sequences from the circular form of the transposon at either the left or the right of the integrated transposon.

Citation: Weaver K, Rice L, Churchward G. 2002. Plasmids and Transposons, p 219-263. In Gilmore M, Clewell D, Courvalin P, Dunny G, Murray B, Rice L (ed), The Enterococci. ASM Press, Washington, DC. doi: 10.1128/9781555817923.ch6
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Tables

Generic image for table
Table 1

Enterococcal cloning vectors

Citation: Weaver K, Rice L, Churchward G. 2002. Plasmids and Transposons, p 219-263. In Gilmore M, Clewell D, Courvalin P, Dunny G, Murray B, Rice L (ed), The Enterococci. ASM Press, Washington, DC. doi: 10.1128/9781555817923.ch6

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