A Replisome's journey through the bacterial chromosome

Abstract

Genome duplication requires the coordinated activity of a multi-component machine, the replisome. In contrast to the background of metabolic diversity across the bacterial domain, the composition and architecture of the bacterial replisome seem to have suffered few changes during evolution. This immutability underlines the replisome's efficiency in copying the genome. It also highlights the success of various strategies inherent to the replisome for responding to stress and avoiding problems during critical stages of DNA synthesis. Here we summarize current understanding of bacterial replisome architecture and highlight the known variations in different bacterial taxa. We then look at the mechanisms in place to ensure that the bacterial replisome is assembled appropriately on DNA, kept together during elongation, and disassembled upon termination. We put forward the idea that the architecture of the replisome may be more flexible that previously thought and speculate on elements of the replisome that maintain its stability to ensure a safe journey from origin to terminus.

Keywords: Bacillus subtilis; DNA polymerase; DNA replication; Escherichia coli; bacteria; chromosome; evolution; replisome.

FIGURE 1

Replisome architecture in bacteria. (A) Architecture of the E. coli replisome, derived from in vitro studies and direct observation in vivo. (B) Architecture of the B. subtilis replisome, predominantly derived from in vitro reconstitution studies.

FIGURE 2

Mechanisms of helicase loading leading to replisome assembly in E. coli. (A) Recognition and melting of the oriC locus during initiation by DnaA. (B) Recognition of abandoned fork structures during replisome reloading by PriA and PriC. All pathways converge on the loading of the replicative helicase DnaB, which acts as an assembly platform for the remaining replisome components.

FIGURE 3

Usage of DNA polymerase during lagging strand synthesis. (A) Schematic of the E. coli replisome during the elongation step of an Okazaki fragment. (B) Lagging strand polymerase meets the RNA primer of the previous Okazaki fragment and stops synthesis. (C) Current model of events following completion of an Okazaki fragment. DNA polymerase is released from the β clamp (step 1) and the same molecule rebinds to a new β clamp to start the next Okazaki fragment (step 2). (D) An alternative model based on evidence from T4 and T7 replisomes. After completing the Okazaki fragment, the DNA polymerase detaches from the rest of the replisome (step 1). A new molecule of DNA polymerase is recruited to the replisome (step 2) and engages in the synthesis of a new Okazaki fragment. In this tentative model, a local pool of “spare” polymerases may facilitate their exchange and additional components may exchange along with the polymerase (not depicted).

FIGURE 4

Mechanism of replication termination in E. coli. (A) Schematic of the E. coli chromosome showing the approximate location of ter sites relative to oriC. Arrowheads indicate the permitted direction of replisome progression. Adapted from Duggin et al., 2008. (B) Mechanism of replisome trapping in the terminus region by Tus-ter. Just two ter sites are shown for clarity but the same mechanism can operate at any ter site. (C) Resolution of DNA structures following replisome convergence during termination.