Principles and concepts of DNA replication in bacteria, archaea, and eukarya

Abstract

The accurate copying of genetic information in the double helix of DNA is essential for inheritance of traits that define the phenotype of cells and the organism. The core machineries that copy DNA are conserved in all three domains of life: bacteria, archaea, and eukaryotes. This article outlines the general nature of the DNA replication machinery, but also points out important and key differences. The most complex organisms, eukaryotes, have to coordinate the initiation of DNA replication from many origins in each genome and impose regulation that maintains genomic integrity, not only for the sake of each cell, but for the organism as a whole. In addition, DNA replication in eukaryotes needs to be coordinated with inheritance of chromatin, developmental patterning of tissues, and cell division to ensure that the genome replicates once per cell division cycle.

Figure 1.

Replication initiation in bacteria and eukaryotes. (A) Most bacteria have a circular chromosome with one origin, although there are exceptions to this. Illustrated here is the E. coli chromosome that has one origin from which two replication forks proceed in opposite directions. (B) Eukaryotes have long linear chromosomes. Bidirectional replication is initiated at multiple origins along each chromosome.

Figure 2.

Origin activation and replisome assembly in bacteria and eukaryotes. (A) Origin activation in eukaryotes is regulated by DDK (Dbf4-Cdc7 kinase) and CDK (cyclin-dependent protein kinase) kinases that have low activity in G₁ phase, and high activity in S phase. (B) Steps in origin activation and replisome assembly in bacteria and eukaryotes. The relatively more complex process of DNA replication in eukaryotes is reflected in the larger number of proteins required to initiate and elongate DNA synthesis from each origin. See text for details.

Figure 3.

Organization of bacterial and eukaryotic replisome machines. (A) Replisome architecture in E. coli. The helicase (DnaB) encircles the lagging strand. Three molecules of Pol III are attached to one clamp loader. The clamp loader binds the helicase and repeatedly assembles β clamps onto primed sites as they are formed by primase. (B) Proposed architecture of a eukaryotic replisome. The MCM2-7 helicase encircles the leading strand; unwinding is aided by association of GINS and Cdc45 with MCM2-7 to form the CMG complex. The RFC clamp loader repeatedly loads PCNA (proliferating cell nuclear antigen) clamps onto lagging-strand primers formed by Pol α-primase. Unlike E. coli, the clamp loader may not form stabile attachments to the replisome. The leading-strand polymerase (Pol ε) is stabilized on DNA by Mrc1. Pol δ replicates the lagging strand. Contacts between Pol δ and other components of the replisome are not yet defined. Mcm10 and Ctf4 contact Pol α-primase.