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Chapter 9 : Initiation of Chromosomal Replication

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Abstract:

The complex process of bacterial chromosomal replication can be divided into several stages: initiation, priming of chain starts, chain elongation, and termination. Since much of what is known about the initiation of bacterial chromosomal replication comes from studies of , this chapter concentrates on initiation in that organism. The roles of the crucial sequence elements in the initiation and regulation of chromosomal replication are discussed in this chapter. DnaA protein, a sequence-specific DNA-binding protein, is responsible for setting in motion the cascade of events for initiating chromosomal replication, including origin recognition, strand opening, and loading of the replicative helicase at the sites of the future bidirectional replication forks. SeqA tetramers must interact properly and form active aggregates for binding to hemimethylated DNA to occur. This SeqA aggregation may be important not only for regulating chromosomal replication, but also for chromosomal segregation. Bypassing the normal, DnaA-dependent initiation of chromosomal replication from via constitutive stable DNA replication relieves the growth arrest of cells lacking sufficient acidic phospholipids. Regulated initiation of chromosomal replication likely involves not only its timing during the cell cycle, but also where it happens within the cell. Recently, significant advances have been made in our knowledge of the initiation of chromosomal replication.

Citation: Camara J, Crooke E. 2005. Initiation of Chromosomal Replication, p 177-192. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch9

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DNA Synthesis
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Figures

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Figure 1

Alignment of bacterial DNA sequences. The sequences were acquired by performing a standard nucleotide-nucleotide BLAST search with the sequence (gi | 42154) on the National Center for Biotechnology Information website (http://www.ncbi.nlm.nih.gov/BLAST/). Matches were found for (gi | 148371), (gi | 40915), (gi | 149827), and Salmonella (gi | 154217). The alignment was performed using AlignX from Vector NTI software (InforMax, Inc.) The solid brackets highlight the traditional 245-bp region. The dotted bracket encompasses an AT-rich region also found important for oriC function. AT-rich 13-mers are indicated with a dotted underline, GATC methylation sites are indicated with a triple bar, and 9-mer DnaA-binding sites are indicatedwith underlining arrows and are labeled (R1 through R4, andM). Shaded regions represent identity to the consensus sequence. Variations from the consensus sequence are indicated by a letter, or by a hyphen (-) for a gap in the sequence. Regions of oriC that lack consensus are represented by N. (Fewer than three sequences contain the same nucleotide at that position.).

Citation: Camara J, Crooke E. 2005. Initiation of Chromosomal Replication, p 177-192. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch9
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Figure 2

Stages in the initiation of DNA replication from .

Citation: Camara J, Crooke E. 2005. Initiation of Chromosomal Replication, p 177-192. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch9
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Figure 3

Mechanisms controlling the initiation of chromosomal replication. Prior to the initiation of a round of chromosomal replication, the amount of ATP-DnaA increases through de novo protein synthesis and possibly through the membrane rejuvenation of ADP-DnaA into ATP-DnaA (indicated by the left-to-right increasing wedge shapes). Once a critical level of DnaA has been reached, replication is initiated at . Three mechanisms then come into play to prevent untimely reinitiation (indicated by the left-to-right decreasing wedge shapes). Immediately following its replication, is sequestered away from the activity of DnaA, with the sequestration of lasting for approximately one-third of the cell cycle. Before sequestration ends, the availability of active DnaA must be decreased to a level too low to promote reinitiation of the replicated origin. This occurs through the binding of DnaA protein to the locus and RIDA conversion of ATP-DnaA protein to inactive ADP-DnaA. The onset of titration of DnaA and the onset of DnaA inactivation by RIDA happen relatively soon after initiation. When in a cell cycle, whether they cease to contribute significantly to the decrease of DnaA potential is unclear. PL, phospholipid.

Citation: Camara J, Crooke E. 2005. Initiation of Chromosomal Replication, p 177-192. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch9
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Figure 4

Positive and negative effects on the initiation potential of DnaA protein. Processes that decrease the initiation potential of DnaA protein are shaded in dark gray. Processes that contribute to the initiation potential of DnaA are shaded in light gray.

Citation: Camara J, Crooke E. 2005. Initiation of Chromosomal Replication, p 177-192. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch9
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