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Chapter 3 : DNA Replication and Cell Cycle

Authors: Si-Houy Lao-Sirieix1, Victoria L. Marsh2, Stephen D. Bell3
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Affiliations: 1: MRC Cancer Cell Unit, Hutchison MRC Research Centre, Hills Road, Cambridge CB2 2XZ, United Kingdom; 2: MRC Cancer Cell Unit, Hutchison MRC Research Centre, Hills Road, Cambridge CB2 2XZ, United Kingdom; 3: MRC Cancer Cell Unit, Hutchison MRC Research Centre, Hills Road, Cambridge CB2 2XZ, United Kingdom
Content Type: Monograph
Publication Year: 2007

Category: Microbial Genetics and Molecular Biology; Environmental Microbiology

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Abstract:

This chapter describes the recent advances that have been made in understanding the biochemical players that facilitate the complex macromolecular process that mediates faithful replication of archaeal chromosomes. The current state of knowledge of the machineries that drive the archaeal cell cycle is discussed. In bacteria, the functional single-stranded DNA-binding proteins (SSBs) is a homotetramer that wraps 65 nucleotides. Pol α, Pol δ, and Pol ε are the major replicative polymerases, with Pol δ acting on the lagging strand and both acting on the leading strand of DNA replication. Sliding clamps are well known for their role in DNA replication, but they also interact with factors involved in other cellular processes, such as DNA repair and recombination, and cell cycle regulators. While an ever-growing body of data has yielded considerable insight into the form and function of the archaeal DNA replication machinery, much less is known about the details of the archaeal cell cycle and its control. Indeed, what little is known appears to be suggesting that diverse mechanisms may be employed to regulate chromosome copy number, to coordinate DNA replication and cell division, and even to mediate the process of cell division itself. Researchers examined nucleoid distribution during the cell cycle, and the results suggested that chromosome segregation was concomitant with DNA replication, as was proposed for , in a mode akin to that employed by bacteria.

Citation: Lao-Sirieix S, Marsh V, Bell S. 2007. DNA Replication and Cell Cycle, p 93-109. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch3
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DNA Replication and Cell Cycle
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Citation: Lao-Sirieix S, Marsh V, Bell S. 2007. DNA Replication and Cell Cycle, p 93-109. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch3
/content/10.1128/9781555815516.ch03.ch03fig01
Figure 1.
Cartoon of the steps involved in DNA replication. Panels A to E describe the assembly of replication fork components at an origin of replication. SSB has been omitted for visual clarity. Panels F and G show detail at a single replication fork.
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10.1128/9781555815516/f0094-01.gif
Image of Figure 1.
Figure 1.

Cartoon of the steps involved in DNA replication. Panels A to E describe the assembly of replication fork components at an origin of replication. SSB has been omitted for visual clarity. Panels F and G show detail at a single replication fork.

Citation: Lao-Sirieix S, Marsh V, Bell S. 2007. DNA Replication and Cell Cycle, p 93-109. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch3
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Figure 2.
Sequence conservation of ORM and mini-ORB (m-ORB) elements at archaeal origins of replication. These serve as binding sites for orthologs of the Cdc6-1 protein. The arrows indicate an imperfect inverted repeat found in the elements. Sso, ; Halo, NRC1; Pab, ).
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Image of Figure 2.
Figure 2.

Sequence conservation of ORM and mini-ORB (m-ORB) elements at archaeal origins of replication. These serve as binding sites for orthologs of the Cdc6-1 protein. The arrows indicate an imperfect inverted repeat found in the elements. Sso, ; Halo, NRC1; Pab, ).

Citation: Lao-Sirieix S, Marsh V, Bell S. 2007. DNA Replication and Cell Cycle, p 93-109. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch3
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Figure 3.
Domain organization of an MCM monomer. The crystal structure of the N-terminal region of has been solved. This region forms a double hexamer; for simplicity, only one hexamer is shown. The DNA-binding fj-hair-pin structures are indicated. HTH, helix-turn-helix domain. Modified from ( ) with permission of the publishers.
10.1128/9781555815516/f0097-01_thmb.gif
10.1128/9781555815516/f0097-01.gif
Image of Figure 3.
Figure 3.

Domain organization of an MCM monomer. The crystal structure of the N-terminal region of has been solved. This region forms a double hexamer; for simplicity, only one hexamer is shown. The DNA-binding fj-hair-pin structures are indicated. HTH, helix-turn-helix domain. Modified from ( ) with permission of the publishers.

Citation: Lao-Sirieix S, Marsh V, Bell S. 2007. DNA Replication and Cell Cycle, p 93-109. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch3
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Figure 4.
Models for the mechanism of DNA unwinding by the MCM helicase. (A) Single hexamer of MCM translocating along single-stranded DNA in a 3to 5direction with the C-terminal AAA domain leading. As it translocates, it unzips DNA ahead of it. A similar situation is shown in B, the difference being that the displaced strand is passed out through an exit channel in the MCM hexamer. An implication of this model is that the motor domain of MCM would bind to double-stranded DNA and the N-terminal domains would bind to single-stranded DNA. (C) A cutaway model of a double hexamer of MCM, with only two of the subunits of each hexamer shown. In this model, the two hexamers are held together by the N-terminal domains, and rather than hexamers moving on DNA, DNA is pumped into the central cavity of the double hexamer. Single-stranded loops of DNA are generated, and these are extruded from the body of the enzyme.
10.1128/9781555815516/f0098-01_thmb.gif
10.1128/9781555815516/f0098-01.gif
Image of Figure 4.
Figure 4.

Models for the mechanism of DNA unwinding by the MCM helicase. (A) Single hexamer of MCM translocating along single-stranded DNA in a 3to 5direction with the C-terminal AAA domain leading. As it translocates, it unzips DNA ahead of it. A similar situation is shown in B, the difference being that the displaced strand is passed out through an exit channel in the MCM hexamer. An implication of this model is that the motor domain of MCM would bind to double-stranded DNA and the N-terminal domains would bind to single-stranded DNA. (C) A cutaway model of a double hexamer of MCM, with only two of the subunits of each hexamer shown. In this model, the two hexamers are held together by the N-terminal domains, and rather than hexamers moving on DNA, DNA is pumped into the central cavity of the double hexamer. Single-stranded loops of DNA are generated, and these are extruded from the body of the enzyme.

Citation: Lao-Sirieix S, Marsh V, Bell S. 2007. DNA Replication and Cell Cycle, p 93-109. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch3
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Figure 5.
Crystal structure of the heterodimeric core primase of . The two subunits are indicated, as are the catalytic aspartate residues. As the regulatory subunit is spatially removed from the catalytic site, it is proposed that this subunit exerts its effect by modulating primer length (see reference ).
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10.1128/9781555815516/f0100-01.gif
Image of Figure 5.
Figure 5.

Crystal structure of the heterodimeric core primase of . The two subunits are indicated, as are the catalytic aspartate residues. As the regulatory subunit is spatially removed from the catalytic site, it is proposed that this subunit exerts its effect by modulating primer length (see reference ).

Citation: Lao-Sirieix S, Marsh V, Bell S. 2007. DNA Replication and Cell Cycle, p 93-109. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch3
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Figure 6.
Model for loading of the PCNA clamp by RF-C. Binding of ATP by RF-C permits formation of the RF-C-PCNA complex. This leads to PCNA opening, presumably by repositioning of the RF-C subunits. DNA is loaded and the clamp resealed. None of these steps require ATP hydrolysis. ATP hydrolysis is, however, required for the next stage, recruitment of DNA polymerase (DNA pol) and release of RF-C.
10.1128/9781555815516/f0103-01_thmb.gif
10.1128/9781555815516/f0103-01.gif
Image of Figure 6.
Figure 6.

Model for loading of the PCNA clamp by RF-C. Binding of ATP by RF-C permits formation of the RF-C-PCNA complex. This leads to PCNA opening, presumably by repositioning of the RF-C subunits. DNA is loaded and the clamp resealed. None of these steps require ATP hydrolysis. ATP hydrolysis is, however, required for the next stage, recruitment of DNA polymerase (DNA pol) and release of RF-C.

Citation: Lao-Sirieix S, Marsh V, Bell S. 2007. DNA Replication and Cell Cycle, p 93-109. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch3
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Figure 7.
A model for the interplay between origin activity and transcriptional regulation of and genes. The model postulates that upon binding to the origins adjacent to their own genes, Cdc6-1 and/or Cdc6-3 exert negative regulation of their own expression. It is further proposed that the gene becomes active at late S phase. This could conceivably be by Cdc6-1 and/or Cdc6-3 activating expression (not shown). In G2, remaining Cdc6-1 and Cdc6-3 protein levels decay and Cdc6-2 levels rise. Cdc6-2 could act as an activator of and and as repressor of its own expression, thereby reducing its own levels, elevating Cdc6-1 and Cdc6-3, and preparing cells for another round of replication following division.
10.1128/9781555815516/f0105-01_thmb.gif
10.1128/9781555815516/f0105-01.gif
Image of Figure 7.
Figure 7.

A model for the interplay between origin activity and transcriptional regulation of and genes. The model postulates that upon binding to the origins adjacent to their own genes, Cdc6-1 and/or Cdc6-3 exert negative regulation of their own expression. It is further proposed that the gene becomes active at late S phase. This could conceivably be by Cdc6-1 and/or Cdc6-3 activating expression (not shown). In G2, remaining Cdc6-1 and Cdc6-3 protein levels decay and Cdc6-2 levels rise. Cdc6-2 could act as an activator of and and as repressor of its own expression, thereby reducing its own levels, elevating Cdc6-1 and Cdc6-3, and preparing cells for another round of replication following division.

Citation: Lao-Sirieix S, Marsh V, Bell S. 2007. DNA Replication and Cell Cycle, p 93-109. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch3
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Tables

DNA Replication and Cell Cycle
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Citation: Lao-Sirieix S, Marsh V, Bell S. 2007. DNA Replication and Cell Cycle, p 93-109. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch3
/content/10.1128/9781555815516.ch03.ch03tab01
Table 1.
Identity of the factors that catalyze the various stages of DNA replication described in Fig. 1
Generic image for table
Table 1.

Identity of the factors that catalyze the various stages of DNA replication described in Fig. 1

Citation: Lao-Sirieix S, Marsh V, Bell S. 2007. DNA Replication and Cell Cycle, p 93-109. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch3
/content/10.1128/9781555815516.ch03.ch03tab02
Table 2.
Composition of SSBs in , , and , highlighting differences in subunit composition and architecture
Generic image for table
Table 2.

Composition of SSBs in , , and , highlighting differences in subunit composition and architecture

Citation: Lao-Sirieix S, Marsh V, Bell S. 2007. DNA Replication and Cell Cycle, p 93-109. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch3

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