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Iteron Plasmids

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  • Authors: Igor Konieczny1, Katarzyna Bury2, Aleksandra Wawrzycka3, Katarzyna Wegrzyn4
  • Editors: Marcelo Tolmasky5, Juan Carlos Alonso6
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, Gdansk, Poland; 2: Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, Gdansk, Poland; 3: Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, Gdansk, Poland; 4: Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, Gdansk, Poland; 5: California State University, Fullerton, CA; 6: Centro Nacional de Biotecnología, Cantoblanco, Madrid, Spain
    • Source: microbiolspec November 2014 vol. 2 no. 6 doi:10.1128/microbiolspec.PLAS-0026-2014
  • Received 13 June 2014 Accepted 19 June 2014 Published 14 November 2014
  • Igor Konieczny, [email protected]
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  • Abstract:

    Iteron-containing plasmids are model systems for studying the metabolism of extrachromosomal genetic elements in bacterial cells. Here we describe the current knowledge and understanding of the structure of iteron-containing replicons, the structure of the iteron plasmid encoded replication initiation proteins, and the molecular mechanisms for iteron plasmid DNA replication initiation. We also discuss the current understanding of control mechanisms affecting the plasmid copy number and how host chaperone proteins and proteases can affect plasmid maintenance in bacterial cells.

  • Citation: Konieczny I, Bury K, Wawrzycka A, Wegrzyn K. 2014. Iteron Plasmids. Microbiol Spectrum 2(6):PLAS-0026-2014. doi:10.1128/microbiolspec.PLAS-0026-2014.

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/content/journal/microbiolspec/10.1128/microbiolspec.PLAS-0026-2014
2014-11-14
2021-03-01

Abstract:

Iteron-containing plasmids are model systems for studying the metabolism of extrachromosomal genetic elements in bacterial cells. Here we describe the current knowledge and understanding of the structure of iteron-containing replicons, the structure of the iteron plasmid encoded replication initiation proteins, and the molecular mechanisms for iteron plasmid DNA replication initiation. We also discuss the current understanding of control mechanisms affecting the plasmid copy number and how host chaperone proteins and proteases can affect plasmid maintenance in bacterial cells.

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Iteron Plasmids
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Citation: Konieczny I, Bury K, Wawrzycka A, Wegrzyn K. 2014. Iteron plasmids. microbiolspec 2(6): doi:10.1128/microbiolspec.PLAS-0026-2014
/content/microbiolspec/10.1128/microbiolspec.PLAS-0026-2014.fig1
FIGURE 1
Scheme of the iteron-containing plasmid origin structure. The direct repeats—iterons—and inverted repeats (IR) are depicted as red arrows. The DUE region of each origin is marked, and repeated sequences within the region are depicted as green triangles. DnaA-box sequences are marked in blue. The region rich in guanidine and cytidine residues (GC-rich) is marked within the origins, if identified. The origins are not drawn to scale.
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FIGURE 1

Scheme of the iteron-containing plasmid origin structure. The direct repeats—iterons—and inverted repeats (IR) are depicted as red arrows. The DUE region of each origin is marked, and repeated sequences within the region are depicted as green triangles. DnaA-box sequences are marked in blue. The region rich in guanidine and cytidine residues (GC-rich) is marked within the origins, if identified. The origins are not drawn to scale.

Source: microbiolspec November 2014 vol. 2 no. 6 doi:10.1128/microbiolspec.PLAS-0026-2014
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FIGURE 2
Structure of replication initiators. DnaA of , RepE54 from mini-F plasmid, π from R6K, and the C-terminal part of the TrfA protein (190-382 aa) of plasmid RK2 are depicted. Structure of the DnaA, RepE54, and π are derived from crystallographic data (PDB entry 1L8Q, 1REP, and 2NRA, respectively). The TrfA model was developed based on homology modeling. The AAA+ domain is colored in blue, the DNA binding domain (DBD) is shown in red, and Winged-Helix domains (WH1 and WH2) are colored in yellow and green, respectively. References and detailed information for crystallographic data of the DnaA, RepE54, π, and TrfA model are given in the text.
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FIGURE 2

Structure of replication initiators. DnaA of , RepE54 from mini-F plasmid, π from R6K, and the C-terminal part of the TrfA protein (190-382 aa) of plasmid RK2 are depicted. Structure of the DnaA, RepE54, and π are derived from crystallographic data (PDB entry 1L8Q, 1REP, and 2NRA, respectively). The TrfA model was developed based on homology modeling. The AAA+ domain is colored in blue, the DNA binding domain (DBD) is shown in red, and Winged-Helix domains (WH1 and WH2) are colored in yellow and green, respectively. References and detailed information for crystallographic data of the DnaA, RepE54, π, and TrfA model are given in the text.

Source: microbiolspec November 2014 vol. 2 no. 6 doi:10.1128/microbiolspec.PLAS-0026-2014
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FIGURE 3
Model of replication initiation: comparison of the processes occurring on the iteron-containing plasmid origin with the replication initiation of bacterial chromosomes. The iteron-containing plasmid origin is recognized by the plasmid-encoded initiator (Rep), which binds cooperatively to the iterons. The interaction of Rep with iterons results in the formation of an open complex and destabilization of the DNA unwinding element (DUE), which creates ssDNA. In RK2, pPS10, F, R6K, P1, and pSC101 the formation of the open complex requires cooperation of the plasmid Rep and host DnaA proteins, while at the chromosomal origin the DnaA protein is sufficient for this process. During the chromosomal origin opening DnaA forms filament on the ssDNA. Helicase delivery and loading requires interaction with the replication initiators; in addition, in the DnaB helicase delivery at the chromosomal as well as at the plasmid RK2 requires the DnaC accessory protein. During the RK2 replication initiation in the host-encoded DnaBC helicase complex is delivered to the DnaA-box sequence through interaction with DnaA, and subsequently the plasmid initiator TrfA translocates the helicase to the opened plasmid origin. The interactions between DnaB and the R6K π protein, F RepE, and pSC101 RepA have also been established as essential for helicase complex formation at the plasmids' origins. The helicase unwinds the DNA double helix, and after a short RNA fragment is synthesized by a primase, a polymerase complex is assembled. Single-stranded DNA binding protein (SSB) is required for replication initiation of both chromosomal and iteron-containing plasmid DNA. The HU/IHF proteins' contribution in DNA replication initiation was omitted in the scheme. For a detailed description see the text.
microbiolspec/2/6/PLAS-0026-2014-fig3_thmb.gif
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FIGURE 3

Model of replication initiation: comparison of the processes occurring on the iteron-containing plasmid origin with the replication initiation of bacterial chromosomes. The iteron-containing plasmid origin is recognized by the plasmid-encoded initiator (Rep), which binds cooperatively to the iterons. The interaction of Rep with iterons results in the formation of an open complex and destabilization of the DNA unwinding element (DUE), which creates ssDNA. In RK2, pPS10, F, R6K, P1, and pSC101 the formation of the open complex requires cooperation of the plasmid Rep and host DnaA proteins, while at the chromosomal origin the DnaA protein is sufficient for this process. During the chromosomal origin opening DnaA forms filament on the ssDNA. Helicase delivery and loading requires interaction with the replication initiators; in addition, in the DnaB helicase delivery at the chromosomal as well as at the plasmid RK2 requires the DnaC accessory protein. During the RK2 replication initiation in the host-encoded DnaBC helicase complex is delivered to the DnaA-box sequence through interaction with DnaA, and subsequently the plasmid initiator TrfA translocates the helicase to the opened plasmid origin. The interactions between DnaB and the R6K π protein, F RepE, and pSC101 RepA have also been established as essential for helicase complex formation at the plasmids' origins. The helicase unwinds the DNA double helix, and after a short RNA fragment is synthesized by a primase, a polymerase complex is assembled. Single-stranded DNA binding protein (SSB) is required for replication initiation of both chromosomal and iteron-containing plasmid DNA. The HU/IHF proteins' contribution in DNA replication initiation was omitted in the scheme. For a detailed description see the text.

Source: microbiolspec November 2014 vol. 2 no. 6 doi:10.1128/microbiolspec.PLAS-0026-2014
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FIGURE 4
Regulation of iteron-containing plasmid replication initiation by the iterons. Rep protein activation occurs by the action of chaperones that convert the Rep dimer to the active monomeric form. Monomers bind to the iteron sequences and perform the initial complex that leads to replication of DNA. Rep protein may also act as a negative regulator of DNA replication by creating “handcuff” structures. Rep proteins couple origins of two separate plasmid particles in a process termed “handcuffing.” In the literature suggestions of chaperone proteins' participation in the “uncuffing” process can be found, but the mechanism of the handcuff structures' reversal is still unclear. For details see the text.
microbiolspec/2/6/PLAS-0026-2014-fig4_thmb.gif
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FIGURE 4

Regulation of iteron-containing plasmid replication initiation by the iterons. Rep protein activation occurs by the action of chaperones that convert the Rep dimer to the active monomeric form. Monomers bind to the iteron sequences and perform the initial complex that leads to replication of DNA. Rep protein may also act as a negative regulator of DNA replication by creating “handcuff” structures. Rep proteins couple origins of two separate plasmid particles in a process termed “handcuffing.” In the literature suggestions of chaperone proteins' participation in the “uncuffing” process can be found, but the mechanism of the handcuff structures' reversal is still unclear. For details see the text.

Source: microbiolspec November 2014 vol. 2 no. 6 doi:10.1128/microbiolspec.PLAS-0026-2014
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FIGURE 5
Regulation of iteron-containing plasmid replication initiation by the auto-repression mechanism. Binding of Rep dimers to inverted repeats inhibits the initiation of transcription starting from the gene promoter. This phenomenon is called auto-repression. An active, monomeric form of Rep protein arises as a result of the action of chaperones. It binds to the iteron sequences that lead to the initiation of DNA replication. Proteases are another factor that may influence the replication process. They limit the amount of both dimer and monomer forms of the Rep protein. For details see the text.
microbiolspec/2/6/PLAS-0026-2014-fig5_thmb.gif
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FIGURE 5

Regulation of iteron-containing plasmid replication initiation by the auto-repression mechanism. Binding of Rep dimers to inverted repeats inhibits the initiation of transcription starting from the gene promoter. This phenomenon is called auto-repression. An active, monomeric form of Rep protein arises as a result of the action of chaperones. It binds to the iteron sequences that lead to the initiation of DNA replication. Proteases are another factor that may influence the replication process. They limit the amount of both dimer and monomer forms of the Rep protein. For details see the text.

Source: microbiolspec November 2014 vol. 2 no. 6 doi:10.1128/microbiolspec.PLAS-0026-2014
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