Modulation of mutagenesis in eukaryotes by DNA replication fork dynamics and quality of nucleotide pools

Abstract

The rate of mutations in eukaryotes depends on a plethora of factors and is not immediately derived from the fidelity of DNA polymerases (Pols). Replication of chromosomes containing the anti-parallel strands of duplex DNA occurs through the copying of leading and lagging strand templates by a trio of Pols α, δ and ε, with the assistance of Pol ζ and Y-family Pols at difficult DNA template structures or sites of DNA damage. The parameters of the synthesis at a given location are dictated by the quality and quantity of nucleotides in the pools, replication fork architecture, transcription status, regulation of Pol switches, and structure of chromatin. The result of these transactions is a subject of survey and editing by DNA repair.

A novel variant of DNA polymerase ζ, Rev3ΔC, highlights differential regulation of Pol32 as a subunit of polymerase δ versus ζ in Saccharomyces cerevisiae

“…It is known that deletion of any of the genes encoding for Rev3, Rev7, Y-family pol Rev1, or Pol32 results in loss of all induced mutagenesis [43]. We showed here that mutagenesis is abolished when rev3ΔC is combined with an additional mutation causing a defect in the catalytic site of Rev3; therefore in vivo the Rev3ΔC/Rev7 polymerase is catalytically active and is responsible for mutation generation.…”

“…Recently it was found that there is a much more intimate relationship between replicative and TLS polymerases than had been imagined: human and yeast pol δ shares two genuine subunits with pol ζ [36,43]. Based on this, we proposed that a switch can occur directly from pol δ to ζ on the platform of two shared subunits (Fig.…”

“…In yeast when the FeS cluster of pol ζ is disrupted, there is a severe reduction of mutagenesis comparable to the complete absence of Rev3 ([32,34], present study). It is possible that this cluster plays a structural role or that the switch is regulated by oxidation–reduction reactions [43]. To better understand how polymerase switches occur in yeast, we created several mutants affecting the CTD of Rev3 (Fig.…”

Eukaryotic genome instability in light of asymmetric DNA replication

“…In the absence of MMR, variants of yeast Pol α with amino acid substitutions in the polymerase active site readily generate point mutations in vitro and in vivo (Niimi et al, 2004, Nick McElhinny et al, 2008, Lujan et al, 2013). Moreover, the Pol α variant preferentially generates errors at replication origins and during synthesis of the lagging strand (Lujan et al, 2013, Nick McElhinny et al, 2008, Waisertreiger et al, 2012). In comparison, Pols δ and ε can both proofread replication errors, and they are more accurate than Pol α in vitro (e.g., see (Fortune et al, 2005, Shcherbakova et al, 2003), reviewed (Kunkel, 2009)).…”

The C-terminal Domain of the DNA Polymerase Catalytic Subunit Regulates the Primase and Polymerase Activities of the Human DNA Polymerase α-Primase Complex

“…The major task of accurate nuclear genome replication in eukaryotes is carried out by B-family DNA polymerases (pols) 5 (2)(3)(4)(5)(6). pol⑀ is indispensable for the assembly of the replisomes at origins (7), pol␣-primase (pol␣-prim) generates primers for the synthesis (8), pol␦ (9) and pol⑀ (10) participate in elongation and bulk DNA synthesis (11)(12)(13), and pol is a key player in the synthesis on templates that are difficult to replicate (14,15).…”