DNA replication fidelity inEscherichia coli: a multi-DNA polymerase affair

Abstract

High accuracy (fidelity) of DNA replication is important for cells to preserve the genetic identity and to prevent the accumulation of deleterious mutations. The error rate during DNA replication is as low as 10−9 to 10−11 errors per base pair. How this low level is achieved is an issue of major interest. This review is concerned with the mechanisms underlying the fidelity of the chromosomal replication in the model system Escherichia coli by DNA polymerase III holoenzyme, with further emphasis on participation of the other, accessory DNA polymerases, of which E. coli contains four (Pols I, II, IV, and V). Detailed genetic analysis of mutation rates revealed that (1) Pol II has an important role as a back‐up proofreader for Pol III, (2) Pols IV and V do not normally contribute significantly to replication fidelity, but can readily do so under conditions of elevated expression, (3) participation of Pols IV and V, in contrast to that of Pol II, is specific to the lagging strand, and (4) Pol I also makes a lagging‐strand‐specific fidelity contribution, limited, however, to the faithful filling of the Okazaki fragment gaps. The fidelity role of the Pol III τ subunit is also reviewed.

The mutagenic footprint of low-fidelity Pol I ColE1 plasmid replication in E. coli reveals an extensive interplay between Pol I and Pol III

“…(2) Topologically, the change in Pol I template preference coincides with the polymerase switch, suggesting that double-strand replication by Pol I and Pol III HE assembly may be mechanistically linked (3). There are precedents for polymerase exchanges during DNA replication: examples of this “polymerase tool belt” scenario include Pol II, Pol IV and Pol V (reviewed in (Fijalkowska et al 2012; Sutton 2010)). While these examples involve highly localized transactions in the context of tolerization to DNA damage, the earlier observation that Pol I is essential for survival in the absence of a functional Pol III α subunit (Maki et al 1989), is consistent with the idea that Pol I can functionally replace the polymerase subunit of Pol III during normal replication.…”

Replisome-mediated Translesion Synthesis and Leading Strand Template Lesion Skipping Are Competing Bypass Mechanisms

“…coli has three TLS polymerases, DNA polymerases (Pols) II, IV (DinB) (7), and V (UmuDЈ 2 UmuC) (8), which have different roles in cellular damage repair and lesion bypass capabilities (9). TLS polymerases are error-prone enzymes, generally lacking proofreading 3Ј 3 5Ј exonuclease activity (although Pol II does have one) and having an active site that accommodates bulky adduct-modified bases (10).…”

“…Pol II and IV are both expressed during normal growth conditions, but neither enzyme appears to play a role in the generation of spontaneous chromosomal mutations (11). All three TLS polymerases are highly induced during the SOS response (9), suggesting their critical participation in a cellular regulatory mechanism to maintain genomic integrity and prevent excessive mutations.…”

The Rate and Molecular Spectrum of Spontaneous Mutations in the GC-Rich Multichromosome Genome of Burkholderia cenocepacia

“…However, as a result of the genetic burden imposed by deleterious mutations, remarkably low mutation rates have evolved across all of life, making detection of these rare events technologically challenging and accurate measures of mutation rates and spectra exceedingly difficult (Kibota and Lynch 1996;Lynch and Walsh 1998;Sniegowski et al 2000;Lynch 2011;Fijalkowska et al 2012;Zhu et al 2014). Until recently, most estimates of mutational properties have been derived indirectly using comparative genomics at putatively neutral sites (Graur and Li 2000;Wielgoss et al 2011) or by extrapolation from small reporter-construct studies (Drake 1991).…”