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Review
. 2018 Mar 14;7(1):23.
doi: 10.3390/antibiotics7010023.

The Macromolecular Machines that Duplicate the Escherichia coli Chromosome as Targets for Drug Discovery

Jon M Kaguni  1
Affiliations
Review

The Macromolecular Machines that Duplicate the Escherichia coli Chromosome as Targets for Drug Discovery

Jon M Kaguni. Antibiotics (Basel). .

Abstract

DNA replication is an essential process. Although the fundamental strategies to duplicate chromosomes are similar in all free-living organisms, the enzymes of the three domains of life that perform similar functions in DNA replication differ in amino acid sequence and their three-dimensional structures. Moreover, the respective proteins generally utilize different enzymatic mechanisms. Hence, the replication proteins that are highly conserved among bacterial species are attractive targets to develop novel antibiotics as the compounds are unlikely to demonstrate off-target effects. For those proteins that differ among bacteria, compounds that are species-specific may be found. Escherichia coli has been developed as a model system to study DNA replication, serving as a benchmark for comparison. This review summarizes the functions of individual E. coli proteins, and the compounds that inhibit them.

Keywords: DNA gyrase; DNA ligase; DNA polymerase I; DNA polymerase III holoenzyme; DNA replication; DnaA; DnaB; DnaC; DnaG; Escherichia coli; SSB; clamp loader; inhibitors; initiation; primase; replication fork; replication origin; replisome; sliding clamp; topoisomerase IV.

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Conflict of interest statement

The author expresses no conflict of interest.

Figures

Figure 1
Figure 1
Replication initiation at the E. coli chromosomal origin involves the recruitment of DnaA, DnaB and DnaC to form the prepriming complex, followed by activation of DnaB, primer formation by primase, and DNA replication by DNA polymerase III holoenzyme. Shown at the top, the replication origin (oriC) of E. coli contains binding sites for Fis and IHF, and the DnaA boxes named R1-R5 that are recognized by DnaA in which the ATP or ADP bound to DnaA may affect the affinities to the respective sites [17,19,90,91]. In contrast, DnaA-ATP and not DnaA-ADP specifically binds to I-, τ- and C-sites. The sites named C3 and C2 overlap R3 and may be separate sites or part of R3 [17,19,90,91]. (1) DnaA, which has four functional domains as noted in the figure of DnaA, recognizes specific DNA sites in E. coli oriC to form a DnaA oligomer. DnaA then unwinds a region containing the 13mers named L, M and R; (2) Domain I of DnaA interacts with the N-terminal domain of DnaB in the DnaB-DnaC complex to load the complex onto the top and bottom DNA strands of the unwound region, forming a macromolecular entity named the prepriming complex. The shaded rectangle represents the space between adjacent DnaB protomers through which the single-stranded DNA passes during helicase loading; (3) Primase interacts with the N-terminal domain of DnaB, which is required for primer synthesis. In the transition to the next step, the open space between adjacent DnaB protomers presumably closes; (4) Primer synthesis (shown as red wavy lines) by primase on the top and bottom strands and the translocation of DnaB leads to the dissociation of DnaC from DnaB; (5) After primer synthesis, primase will dissociate from DnaB as the primer is bound by DNA polymerase III holoenzyme. DnaB will move to the junction of each replication fork; (6) DNA polymerase III holoenzyme extends the primers for the synthesis of each leading strand. DnaB at the junction of each replication fork unwinds the parental duplex DNA. The transient interaction of DnaB with primase as the helicase moves leads to the synthesis of subsequent primers that are extended by DNA polymerase III holoenzyme in the synthesis of Okazaki fragments. The dashed lines represent the contacts between two units of DNA polymerase III holoenzyme, forming a dimer in the coordinated synthesis of the leading and lagging strands.
Figure 2
Figure 2
Subunit composition and their interactions of DNA polymerase III holoenzyme (reviewed in [207,218,224]). The subassemblies of DNA polymerase III holoenzyme are the sliding clamp composed of two DnaN or β subunits, the clamp loader or DnaX complex composed of seven subunits, and DNA polymerase III core containing the α, ε and θ subunits. The diagram also summarizes how these subunits interact within each subassembly and between subassemblies.
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