Initiating DNA replication: a matter of prime importance

Stephen D Bell

doi:10.1042/bst20180627

Abstract

It has been known for decades that the principal replicative DNA polymerases that effect genome replication are incapable of starting DNA synthesis de novo. Rather, they require a 3′-OH group from which to extend a DNA chain. Cellular DNA replication systems exploit a dedicated, limited processivity RNA polymerase, termed primase, that synthesizes a short oligoribonucleotide primer which is then extended by a DNA polymerase. Thus, primases can initiate synthesis, proceed with primer elongation for a short distance then transfer the primer to a DNA polymerase. Despite these well-established properties, the mechanistic basis of these dynamic behaviours has only recently been established. In the following, the author will describe recent insights from studies of the related eukaryotic and archaeal DNA primases. Significantly, the general conclusions from these studies likely extend to a broad class of extrachromosomal element-associated primases as well as the human primase-related DNA repair enzyme, PrimPol.

Highlights

As with the rest of the DNA replication machinery, the archaeal DNA primases have an orthologous relationship to their counterparts in eukaryotes and are structurally distinct from the primases encoded in bacterial genomes [1]
The bacterial primase, DnaG, is based on a ‘Toprim’ fold — a module of roughly 100 amino acids that is found in topoisomerases, bacterial primases and several nucleases [2]
The true DNA primase of archaeal species is based on a heterodimeric assembly of two subunits homologous to the PriS and PriL subunits of the eukaryotic primase assembly [4]

Summary

Introduction

As with the rest of the DNA replication machinery, the archaeal DNA primases have an orthologous relationship to their counterparts in eukaryotes and are structurally distinct from the primases encoded in bacterial genomes [1]. The structure of an initiation complex of RNA polymerase from the bacterium Thermus thermophilus revealed that the initiating nucleotide bound the same site as that occupied by the growing 30-end of an elongating RNA chain [14]. Subsequent biochemical experiments revealed that mutation of R72 to alanine abolished nucleotide interaction and that reconstituted PriSLX containing PriX R72A caused the primase to be initiation defective but elongation competent.

Results

Conclusion