Repriming DNA synthesis: an intrinsic restart pathway that maintains efficient genome replication

Abstract

To bypass a diverse range of fork stalling impediments encountered during genome replication, cells possess a variety of DNA damage tolerance (DDT) mechanisms including translesion synthesis, template switching, and fork reversal. These pathways function to bypass obstacles and allow efficient DNA synthesis to be maintained. In addition, lagging strand obstacles can also be circumvented by downstream priming during Okazaki fragment generation, leaving gaps to be filled post-replication. Whether repriming occurs on the leading strand has been intensely debated over the past half-century. Early studies indicated that both DNA strands were synthesised discontinuously. Although later studies suggested that leading strand synthesis was continuous, leading to the preferred semi-discontinuous replication model. However, more recently it has been established that replicative primases can perform leading strand repriming in prokaryotes. An analogous fork restart mechanism has also been identified in most eukaryotes, which possess a specialist primase called PrimPol that conducts repriming downstream of stalling lesions and structures. PrimPol also plays a more general role in maintaining efficient fork progression. Here, we review and discuss the historical evidence and recent discoveries that substantiate repriming as an intrinsic replication restart pathway for maintaining efficient genome duplication across all domains of life.

APOBEC mutagenesis is low in most types of non-B DNA structures, unlike other types of cancer mutagenesis

“…This polymerase is known to shield DNA from APOBEC/AID mutagenesis 37 . PrimPol is known for its implication in eukaryotic DNA damage tolerance 38 , displaying both translesion synthesis and (re)-priming properties 39 . PrimPol is required for replicating G-quadruplexes 40 and presumably other types of non-canonical DNA structures 41 .…”

SV40 T antigen helicase domain regions responsible for oligomerisation regulate Okazaki fragment synthesis initiation

“…Studies of the mechanism of DNA replication and how eukaryotes duplicate their genomes accurately during the cell cycle are at the forefront of molecular biology research [1][2][3][4][5]. The replication of the genomes of small eukaryotic DNA viruses such as simian virus 40 (SV40) and other polyomaviruses has served as a model for the understanding of cellular DNA replication of their hosts [6][7][8].…”

“…Pol-prim is a heterotetrameric protein complex consisting of p180, p68, p58 and p48 with the two largest subunits forming the Pol a-core and the two smallest making up the primase with its two subunits also called Prim 1 (p48) and Prim 2 (p58) [1,10,25]. Since DNA polymerases lack the ability to perform de novo DNA synthesis without a free 3' hydroxyl group, eukaryotic replicative DNA polymerases utilise the free OH group of an RNA primer synthesised by the primase function of Pol-prim [26].…”

APOBEC mutagenesis is low in most types of non-B DNA structures

“…This polymerase is known to shield DNA from APOBEC/AID mutagenesis ( Pilzecker et al., 2016 ). PrimPol is known for its implication in eukaryotic DNA damage tolerance ( Bailey et al., 2019 ), displaying both translesion synthesis and (re)-priming properties ( Bainbridge et al., 2021 ). PrimPol is required for replicating G-quadruplexes ( Schiavone et al., 2016 ) and presumably other types of non-canonical DNA structures ( Šviković et al., 2019 ).…”