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Plasmid Rolling-Circle Replication

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  • Authors: J. A. Ruiz-Masó1, C. MachóN2, L. Bordanaba-Ruiseco4, M. Espinosa5, M. Coll6, G. Del Solar8
  • Editors: Marcelo Tolmasky9, Juan Carlos Alonso10
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; 2: Institute for Research in Biomedicine (IRB-Barcelona), Baldiri Reixac 10-12, 08028 Barcelona, Spain; 3: Institut de Biologia Molecular de Barcelona (CSIC), Baldiri Reixac 10-12, 08028 Barcelona, Spain; 4: Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; 5: Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; 6: Institute for Research in Biomedicine (IRB-Barcelona), Baldiri Reixac 10-12, 08028 Barcelona, Spain; 7: Institut de Biologia Molecular de Barcelona (CSIC), Baldiri Reixac 10-12, 08028 Barcelona, Spain; 8: Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; 9: California State University, Fullerton, CA; 10: Centro Nacional de Biotecnología, Cantoblanco, Madrid, Spain
  • Source: microbiolspec February 2015 vol. 3 no. 1 doi:10.1128/microbiolspec.PLAS-0035-2014
  • Received 17 December 2014 Accepted 18 December 2014 Published 20 February 2015
  • G. del Solar, gdelsolar@cib.csic.es
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  • Abstract:

    Plasmids are DNA entities that undergo controlled replication independent of the chromosomal DNA, a crucial step that guarantees the prevalence of the plasmid in its host. DNA replication has to cope with the incapacity of the DNA polymerases to start DNA synthesis, and different replication mechanisms offer diverse solutions to this problem. Rolling-circle replication (RCR) is a mechanism adopted by certain plasmids, among other genetic elements, that represents one of the simplest initiation strategies, that is, the nicking by a replication initiator protein on one parental strand to generate the primer for leading-strand initiation and a single priming site for lagging-strand synthesis. All RCR plasmid genomes consist of a number of basic elements: leading strand initiation and control, lagging strand origin, phenotypic determinants, and mobilization, generally in that order of frequency. RCR has been mainly characterized in Gram-positive bacterial plasmids, although it has also been described in Gram-negative bacterial or archaeal plasmids. Here we aim to provide an overview of the RCR plasmids' lifestyle, with emphasis on their characteristic traits, promiscuity, stability, utility as vectors, etc. While RCR is one of the best-characterized plasmid replication mechanisms, there are still many questions left unanswered, which will be pointed out along the way in this review.

  • Citation: Ruiz-Masó J, MachóN C, Bordanaba-Ruiseco L, Espinosa M, Coll M, Del Solar G. 2015. Plasmid Rolling-Circle Replication. Microbiol Spectrum 3(1):PLAS-0035-2014. doi:10.1128/microbiolspec.PLAS-0035-2014.

Key Concept Ranking

Mobile Genetic Elements
0.87199855
DNA Synthesis
0.5843034
Genetic Elements
0.5813324
Chromosomal DNA
0.56957895
0.87199855

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/content/journal/microbiolspec/10.1128/microbiolspec.PLAS-0035-2014
2015-02-20
2017-11-24

Abstract:

Plasmids are DNA entities that undergo controlled replication independent of the chromosomal DNA, a crucial step that guarantees the prevalence of the plasmid in its host. DNA replication has to cope with the incapacity of the DNA polymerases to start DNA synthesis, and different replication mechanisms offer diverse solutions to this problem. Rolling-circle replication (RCR) is a mechanism adopted by certain plasmids, among other genetic elements, that represents one of the simplest initiation strategies, that is, the nicking by a replication initiator protein on one parental strand to generate the primer for leading-strand initiation and a single priming site for lagging-strand synthesis. All RCR plasmid genomes consist of a number of basic elements: leading strand initiation and control, lagging strand origin, phenotypic determinants, and mobilization, generally in that order of frequency. RCR has been mainly characterized in Gram-positive bacterial plasmids, although it has also been described in Gram-negative bacterial or archaeal plasmids. Here we aim to provide an overview of the RCR plasmids' lifestyle, with emphasis on their characteristic traits, promiscuity, stability, utility as vectors, etc. While RCR is one of the best-characterized plasmid replication mechanisms, there are still many questions left unanswered, which will be pointed out along the way in this review.

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FIGURE 1

(A) A model for plasmid RCR based on pMV158 and pT181 replicons. Detailed information about the RCR process is given in the text. In the pMV158 replication model, a possible mechanism is shown in which, upon assembly and cleavage at the nick site, the hexameric ring of RepB encircles one of the plasmid strands within the central channel. As discussed in the text, the strand enclosure may confer high processivity to the replisome complex. The RepB-mediated mechanism that, at the termination step, yields the dsDNA replication product and the ssDNA intermediate, as well as the mechanism of RepB inactivation, remain undisclosed (dotted arrow with ? symbol). (B) Scheme of the s and of the adjacent regions of the pMV158 and pT181 RCR plasmids. The symbols used are as follows: direct repeats in the replication region are indicated by solid boxed arrows; the inverted arrows represent the two arms of the inverted repeat elements; promoters are indicated by open arrowheads. The AT- and GC-rich sequences (A+T and G+C, respectively) are also indicated. The dotted line above the pMV158 map indicates that the direct repeats of the locus are separated by 84 bp from the nick site. SSB, single-stranded DNA binding protein. doi:10.1128/microbiolspec.PLAS-0035-2014.f1

Source: microbiolspec February 2015 vol. 3 no. 1 doi:10.1128/microbiolspec.PLAS-0035-2014
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FIGURE 2

Functional organization of the RCR plasmids. Plasmids representative of the different families are shown. The arrows point to the direction of transcription (black) or the direction of replication (red) from the (leading strand) and (lagging strand). Inside the boxes, is the replication gene; represents the copy number control gene(s); is the double-strand origin of replication; is the single-strand origin of replication; and are chloramphenicol- and tetracycline-resistant genes, respectively; represents the conjugative mobilization gene; indicates an open reading frame with unknown homology. The positions of the copy number control genes and of pGA1, and of the gene of pTX14-2 are also indicated. doi:10.1128/microbiolspec.PLAS-0035-2014.f2

Source: microbiolspec February 2015 vol. 3 no. 1 doi:10.1128/microbiolspec.PLAS-0035-2014
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FIGURE 3

Domain structure of the Rep proteins from RCR plasmids. Predicted and observed secondary structures of the replication proteins of different RCR plasmids and of the Rep proteins from the adeno associated virus (AAV) and bovine papillomavirus (BPV). The amino-terminal end (N) and the number of amino acids are indicated for each of the proteins analyzed. The predicted or observed α-helices and β-strands are represented as red and green bars, respectively. The 3-helices are represented as blue bars. Conserved amino acid residues of the active site involved in metal binding (HUH) and in the endonucleolytic activity are indicated in the protein maps. The conserved Walker A, B, and C motifs are indicated in the proteins with a helicase domain. The limits of the origin binding domain (OBD) and of the oligomerization domain (OD) are indicated in the protein maps of RepB, Rep68, and E1. The additional line below the sequence of RepB, Rep68, and E1 shows the secondary structure present in the crystal structure of the protein (PDB entry code is given in the figure). Plasmidic Rep proteins were aligned by the metal binding HUH motif. However, viral Reps were aligned with RepB by the all-helical OD domain due to the structural similarity found in this region. doi:10.1128/microbiolspec.PLAS-0035-2014.f3

Source: microbiolspec February 2015 vol. 3 no. 1 doi:10.1128/microbiolspec.PLAS-0035-2014
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FIGURE 4

Cartoon representation of the structure of RepB obtained by X-ray crystallography. (A) Top (left) and side (right) views of the RepB hexamer. The locations of the OBD (continuous line) and of the OD (dotted line) are also indicated in the two views. The position of the hinge connecting both domains is indicated in the side view. (B) Top (left) and side (right) views of the electrostatic potential on the solvent-accessible surface of the RepB hexamer structure. The location of the crevice is indicated. doi:10.1128/microbiolspec.PLAS-0035-2014.f4

Source: microbiolspec February 2015 vol. 3 no. 1 doi:10.1128/microbiolspec.PLAS-0035-2014
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