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Chapter 9 : Resolution of Multimeric Forms of Circular Plasmids and Chromosomes

Authors: Estelle Crozat1, Florian Fournes2, François Cornet3, Bernard Hallet4, Philippe Rousseau5
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Affiliations: 1: Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, F-31062 Toulouse, France; 2: Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, F-31062 Toulouse, France; 3: CNRS, Laboratoire de Microbiologie et Génétique Moléculaires, F-31062 Toulouse, France; 4: Institut des Sciences de la Vie, UCLouvain, 4/5 L7.07.06 Place Croix du Sud, B-1348 Louvain-la-Neuve, Belgium; 5: Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, F-31062 Toulouse, France
Content Type: Monograph
Publication Year: 2015

Category: Clinical Microbiology

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Abstract:

One of the serious disadvantages of circular plasmids and chromosomes is their high sensitivity to rearrangements caused by homologous recombination. Odd numbers of recombinational exchanges occurring during or after replication of a circular replicon result in the formation of a dimeric molecule in which the two copies of the replicon are fused in a head-to-tail configuration ( Fig. 1 ). If they are not converted back to monomers, the dimers of replicons may fail to correctly segregate at the time of cell division.

Citation: Crozat E, Fournes F, Cornet F, Hallet B, Rousseau P. 2015. Resolution of Multimeric Forms of Circular Plasmids and Chromosomes, p 157-173. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0025-2014
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Resolution of Multimeric Forms of Circular Plasmids and Chromosomes
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Citation: Crozat E, Fournes F, Cornet F, Hallet B, Rousseau P. 2015. Resolution of Multimeric Forms of Circular Plasmids and Chromosomes, p 157-173. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0025-2014
/content/10.1128/9781555818982.chap9.fig9-1
Figure 1
Formation of plasmid dimers and their stability in the cell. Dimers of plasmids or chromosomes are formed by homologous recombination (HR) during replication and are later resolved by site-specific recombination (SSR). Origins are shown by a circle, and site-specific recombination sites by a black and white square. The accumulation of plasmid dimers in the cell leads to an increase in plasmid loss compared to monomeric plasmids.
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Figure 1

Formation of plasmid dimers and their stability in the cell. Dimers of plasmids or chromosomes are formed by homologous recombination (HR) during replication and are later resolved by site-specific recombination (SSR). Origins are shown by a circle, and site-specific recombination sites by a black and white square. The accumulation of plasmid dimers in the cell leads to an increase in plasmid loss compared to monomeric plasmids.

Citation: Crozat E, Fournes F, Cornet F, Hallet B, Rousseau P. 2015. Resolution of Multimeric Forms of Circular Plasmids and Chromosomes, p 157-173. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0025-2014
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Figure 2
Site-specific recombination by serine recombinases. Structure of the recombination sites of Tn3 and γδ recombinases (top) and the β recombinase and Sin family (bottom). Sequences are shown with arrows, and their length is (bp) indicated nearby. The genes coding for the recombinases are located downstream (rec). Hbsu (red) depicts a binding site for the accessory protein. The primary structure of a typical serine recombinase (top), showing the catalytic serine in a circle; other amino acids implicated in catalysis are also indicated (bottom). The scheme depicts the four principal steps of recombination by serine recombinase: four recombinases bind on their sites and form the synapse; the four strands are cut and bound covalently to the catalytic serines (red dot), which is followed by a 180° rotation of two of the subunits and rejoining of the DNA strands.
10.1128/9781555818982/fig9-2_thmb.gif
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Image of Figure 2
Figure 2

Site-specific recombination by serine recombinases. Structure of the recombination sites of Tn3 and γδ recombinases (top) and the β recombinase and Sin family (bottom). Sequences are shown with arrows, and their length is (bp) indicated nearby. The genes coding for the recombinases are located downstream (rec). Hbsu (red) depicts a binding site for the accessory protein. The primary structure of a typical serine recombinase (top), showing the catalytic serine in a circle; other amino acids implicated in catalysis are also indicated (bottom). The scheme depicts the four principal steps of recombination by serine recombinase: four recombinases bind on their sites and form the synapse; the four strands are cut and bound covalently to the catalytic serines (red dot), which is followed by a 180° rotation of two of the subunits and rejoining of the DNA strands.

Citation: Crozat E, Fournes F, Cornet F, Hallet B, Rousseau P. 2015. Resolution of Multimeric Forms of Circular Plasmids and Chromosomes, p 157-173. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0025-2014
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Figure 3
Site-specific recombination by tyrosine recombinases. Structure of principal recombination sites from tyrosine recombinase family. Symbols are the same as in Fig. 2 . The primary structure of a typical tyrosine recombinase (top), showing the catalytic tyrosine in a circle; other amino-acids implicated in catalysis are also indicated. Two distinct protein domains are shown: the DNA binding domain (DBD) and another DNA binding domain containing the catalytic domain (DBD + CD) (bottom). The scheme depicts the principal steps of recombination by tyrosine recombinase: four recombinases bind on their sites and form the synapse; cleavage occurs first on only two DNA strands, catalyzed by one active pair of recombinases in the teramer (XerC or XerD in the case of , , , and ). A transient Holliday junction is formed after a first strand exchange and is isomerized to allow the cleavage of the two other strands by the other pair of recombinases. The second strand exchange takes place, and the complex dissociates.
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Image of Figure 3
Figure 3

Site-specific recombination by tyrosine recombinases. Structure of principal recombination sites from tyrosine recombinase family. Symbols are the same as in Fig. 2 . The primary structure of a typical tyrosine recombinase (top), showing the catalytic tyrosine in a circle; other amino-acids implicated in catalysis are also indicated. Two distinct protein domains are shown: the DNA binding domain (DBD) and another DNA binding domain containing the catalytic domain (DBD + CD) (bottom). The scheme depicts the principal steps of recombination by tyrosine recombinase: four recombinases bind on their sites and form the synapse; cleavage occurs first on only two DNA strands, catalyzed by one active pair of recombinases in the teramer (XerC or XerD in the case of , , , and ). A transient Holliday junction is formed after a first strand exchange and is isomerized to allow the cleavage of the two other strands by the other pair of recombinases. The second strand exchange takes place, and the complex dissociates.

Citation: Crozat E, Fournes F, Cornet F, Hallet B, Rousseau P. 2015. Resolution of Multimeric Forms of Circular Plasmids and Chromosomes, p 157-173. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0025-2014
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Figure 4
Topology of various recombinational synapses. Examples of synapses formed during recombination by two main families of serine recombinase and one of tyrosine recombinase are shown. Main recombination sites are colored (blue and green/purple), and the accessory sequences are shown as a thick line. The precise configuration of the synapses are drawn below, with serine recombinase in blue, Hbsu in orange, XerC and Xer in green and purple, PepA in dark green, and ArgR in red.
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Image of Figure 4
Figure 4

Topology of various recombinational synapses. Examples of synapses formed during recombination by two main families of serine recombinase and one of tyrosine recombinase are shown. Main recombination sites are colored (blue and green/purple), and the accessory sequences are shown as a thick line. The precise configuration of the synapses are drawn below, with serine recombinase in blue, Hbsu in orange, XerC and Xer in green and purple, PepA in dark green, and ArgR in red.

Citation: Crozat E, Fournes F, Cornet F, Hallet B, Rousseau P. 2015. Resolution of Multimeric Forms of Circular Plasmids and Chromosomes, p 157-173. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0025-2014
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Figure 5
Resolution of chromosome dimers. During chromosome replication, single- or double-strand breaks appear that necessitate homologous recombination to be repaired. This leads to the formation of dimers of chromosomes, which are resolved by XerC (green) and XerD (purple) after the activation of XerD by FtsK (orange), localized at the septum. Cell division can then take place and maintain two integrate copies of the chromosome. Origins of replication are represented as green and black dots, replication forks as black complexes with white arrows indicating replication direction, and the site as a green and purple square.
10.1128/9781555818982/fig9-5_thmb.gif
10.1128/9781555818982/fig9-5.gif
Image of Figure 5
Figure 5

Resolution of chromosome dimers. During chromosome replication, single- or double-strand breaks appear that necessitate homologous recombination to be repaired. This leads to the formation of dimers of chromosomes, which are resolved by XerC (green) and XerD (purple) after the activation of XerD by FtsK (orange), localized at the septum. Cell division can then take place and maintain two integrate copies of the chromosome. Origins of replication are represented as green and black dots, replication forks as black complexes with white arrows indicating replication direction, and the site as a green and purple square.

Citation: Crozat E, Fournes F, Cornet F, Hallet B, Rousseau P. 2015. Resolution of Multimeric Forms of Circular Plasmids and Chromosomes, p 157-173. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0025-2014
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