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EcoSal Plus

Domain 4:

Synthesis and Processing of Macromolecules

Initiation of DNA Replication

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  • Authors: Alan C. Leonard1, and Julia E. Grimwade2
  • Editor: Susan T. Lovett3
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Florida Institute of Technology, Department of Biological Sciences, Melbourne, FL 32901–6975; 2: Florida Institute of Technology, Department of Biological Sciences, Melbourne, FL 32901–6975; 3: Brandeis University, Waltham, MA
  • Received 05 August 2009 Accepted 28 October 2009 Published 05 January 2010
  • Address correspondence to Alan C. Leonard aleonard@fit.edu
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  • Abstract:

    In recent years it has become clear that complex regulatory circuits control the initiation step of DNA replication by directing the assembly of a multicomponent molecular machine (the orisome) that separates DNA strands and loads replicative helicase at , the unique chromosomal origin of replication. This chapter discusses recent efforts to understand the regulated protein-DNA interactions that are responsible for properly timed initiation of chromosome replication. It reviews information about newly identified nucleotide sequence features within and the new structural and biochemical attributes of the bacterial initiator protein DnaA. It also discusses the coordinated mechanisms that prevent improperly timed DNA replication. Identification of the genes that encoded the initiators came from studies on temperature-sensitive, conditional-lethal mutants of , in which two DNA replication-defective phenotypes, "immediate stop" mutants and "delayed stop" mutants, were identified. The kinetics of the delayed stop mutants suggested that the defective gene products were required specifically for the initiation step of DNA synthesis, and subsequently, two genes, and , were identified. The DnaA protein is the bacterial initiator, and in , the DnaC protein is required to load replicative helicase. Regulation of DnaA accessibility to , the ordered assembly and disassembly of a multi-DnaA complex at , and the means by which DnaA unwinds remain important questions to be answered and the chapter discusses the current state of knowledge on these topics.

  • Citation: Leonard A, Grimwade J. 2010. Initiation of DNA Replication, EcoSal Plus 2010; doi:10.1128/ecosalplus.4.4.1

Key Concept Ranking

DNA Synthesis
0.78661543
Bacterial Proteins
0.57747155
DNA Polymerase III
0.4984373
0.78661543

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/content/journal/ecosalplus/10.1128/ecosalplus.4.4.1
2010-01-05
2017-04-27

Abstract:

In recent years it has become clear that complex regulatory circuits control the initiation step of DNA replication by directing the assembly of a multicomponent molecular machine (the orisome) that separates DNA strands and loads replicative helicase at , the unique chromosomal origin of replication. This chapter discusses recent efforts to understand the regulated protein-DNA interactions that are responsible for properly timed initiation of chromosome replication. It reviews information about newly identified nucleotide sequence features within and the new structural and biochemical attributes of the bacterial initiator protein DnaA. It also discusses the coordinated mechanisms that prevent improperly timed DNA replication. Identification of the genes that encoded the initiators came from studies on temperature-sensitive, conditional-lethal mutants of , in which two DNA replication-defective phenotypes, "immediate stop" mutants and "delayed stop" mutants, were identified. The kinetics of the delayed stop mutants suggested that the defective gene products were required specifically for the initiation step of DNA synthesis, and subsequently, two genes, and , were identified. The DnaA protein is the bacterial initiator, and in , the DnaC protein is required to load replicative helicase. Regulation of DnaA accessibility to , the ordered assembly and disassembly of a multi-DnaA complex at , and the means by which DnaA unwinds remain important questions to be answered and the chapter discusses the current state of knowledge on these topics.

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Figures

Image of Figure 1
Figure 1

Chromosome configurations for four different growth rates (20, 40, 50, and 80 min) are shown. Cell cycle time is indicated by the time line at the top of the figure. For all growth rates, the C period is 40 min and the D period is 20 min. In cells growing with doubling times of less than 40 min, a new round of chromosome replication is initiated before completion of the previous round, resulting in multifork replication (see 30- and 20-min doubling times; bottom two rows). Faster growth rates produce larger cells with increased numbers of origins and increased DNA content per cell. Cells growing more slowly than C + D minutes (e.g., 60 min) have gaps in DNA synthesis (see 80-min doubling time, top row). The time of initiation is independent of cell cycle time, and cells initiate chromosome replication when they accumulate sufficient mass per origin. Initiating origins are marked by colored ovals. For all rows, the oldest (parental) chromosome is black, the next oldest is red, the next oldest is blue, and the youngest is green.

Citation: Leonard A, Grimwade J. 2010. Initiation of DNA Replication, EcoSal Plus 2010; doi:10.1128/ecosalplus.4.4.1
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Image of Figure 2
Figure 2

(Left) A schematic illustration of DnaA is shown. Domain I is bright blue, domain II is light blue, domain III is green, and domain IV is yellow. Locations of key structural features, described in the text, are labeled. (Right) Model of the binding of a DnaA dimer to two adjacent 9-mer recognition sites in DNA (shown by black line). The binding of ATP to DnaA causes a structural change in domain III, such that the arginine finger of box VII interacts with the ATP bound to the adjacent DnaA molecule. Interaction between the two N-terminal domains is also shown.

Citation: Leonard A, Grimwade J. 2010. Initiation of DNA Replication, EcoSal Plus 2010; doi:10.1128/ecosalplus.4.4.1
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Image of Figure 3
Figure 3

(Top) The unique origin of replication, , is located between the genes for and on the chromosome. The top numbers indicate the nucleotide position in the genomic sequence. The arrows indicate the direction of transcription. (Bottom) At the left side of , a gold overline indicates the location of the Duplex Unwinding Element (DUE); the AT-rich 13-mer repeats are highlighted in pink, and the ATP-DnaA Speck-Messer (S-M) sites are outlined by black boxes. The 11 GATC sequences highlighted in dark purple are the sites for SeqA binding and DAM methylation. High-affinity DnaA binding sites (R1, R2, and R4) are indicated by bright blue, while low-affinity nondiscriminatory R boxes are drawn in dark blue. The τ-sites and I sites, highlighted in violet, preferentially bind DnaA-ATP. The binding sites for the DNA bending proteins IHF and Fis are highlighted in green and red, respectively.

Citation: Leonard A, Grimwade J. 2010. Initiation of DNA Replication, EcoSal Plus 2010; doi:10.1128/ecosalplus.4.4.1
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Image of Figure 4A
Figure 4A

(A) Factors or processes that affect DnaA-ATP availability include those that increase DnaA-ATP levels (shown in green): new transcription, the DARS regions, and acidic phospholipids. Factors or processes that decrease availability of DnaA-ATP (shown in red) include sequestration of the promoter region to prevent new synthesis, RIDA/Hda-mediated hydrolysis of DnaA-ATP to DnaA-ADP, titration of DnaA to the locus and other chromosomal titration sites, and long-term association with the membrane, removing DnaA from the pool of protein in the cell.

Citation: Leonard A, Grimwade J. 2010. Initiation of DNA Replication, EcoSal Plus 2010; doi:10.1128/ecosalplus.4.4.1
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Image of Figure 4B
Figure 4B

(B) Regulators of complex assembly that act by inhibiting DnaA from binding to low-affinity sites (Fis and SeqA), or by directly preventing unwinding by interacting with DnaA (Dps) or the 13-mer region (IciA) are indicated by labeled octagons and shades of red. Regulators that stimulate orisome formation by facilitating DnaA binding to low-affinity sites (IHF, DiaA) or stimulating unwinding (HU, transcription from the promoter) are indicated by labeled circles and shades of green. High-affinity DnaA boxes are indicated by bright-blue boxes; low-affinity nondiscriminatory R boxes are drawn as dark-blue boxes; and τ and I sites, which have a preference for DnaA-ATP, are drawn as purple boxes.

Citation: Leonard A, Grimwade J. 2010. Initiation of DNA Replication, EcoSal Plus 2010; doi:10.1128/ecosalplus.4.4.1
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Image of Figure 5A
Figure 5A

(A) The orisome is assembled in stages. In stage 1, DnaA (blue circles) is bound to R1, R2, and R4, and Fis (red octagon) is bound to its cognate site. DnaA accumulates at the higher-affinity sites (stage 2) until enough DnaA is present to displace Fis and allow binding of IHF (green circle) to its site between R1 and τ1 (stage 3). Binding of IHF stimulates DnaA binding to all the lower-affinity sites, with the τ-sites and I sites binding DnaA-ATP. It is not known what form of DnaA binds to the other sites, and this ambiguity is indicated by a question mark. Full occupation of by DnaA results in DNA strand separation in the DUE (gold) and binding of DnaA-ATP to the single-stranded region, forming the bacterial pre-RC (stage 4). Attributes of the DnaA binding sites are indicated by colors, as described in the legend to Fig. 4B .

Citation: Leonard A, Grimwade J. 2010. Initiation of DNA Replication, EcoSal Plus 2010; doi:10.1128/ecosalplus.4.4.1
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Image of Figure 5B
Figure 5B

(B) Disassembly of the orisome and resetting of to the ORC also occurs in stages. DnaA is removed from the pre-RC (stage 4) by helicase translocation and replication fork movement. Replication of causes hemimethylation of the 11 GATC residues (small black circles) (stage 5), creating binding sites for SeqA (purple octagon) (stage 6). The displaced DnaA rebinds the high-affinity sites (stage 6) but is blocked from rebinding to the weaker sites. The end of sequestration results in resetting of the ORC (stage 1). The excess DnaA displaced from the pre-RC binds other chromosomal sites, including the locus, and is inactivated by RIDA/Hda. Hda is shown by dark red ovals, and the β-clamp is shown by a yellow circle. DnaA-ADP can be recharged to DnaA-ATP by DARS or by acidic phospholipids.

Citation: Leonard A, Grimwade J. 2010. Initiation of DNA Replication, EcoSal Plus 2010; doi:10.1128/ecosalplus.4.4.1
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