The fidelity of DNA synthesis by eukaryotic replicative and translesion synthesis polymerases

Abstract

In their seminal publication describing the structure of the DNA double helix [1], Watson and Crick wrote what may be one of the greatest understatements in the scientific literature, namely that "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material." Half a century later, we more fully appreciate what a huge challenge it is to replicate six billion nucleotides with the accuracy needed to stably maintain the human genome over many generations. This challenge is perhaps greater than was realized 50 years ago, because subsequent studies have revealed that the genome can be destabilized not only by environmental stresses that generate a large number and variety of potentially cytotoxic and mutagenic lesions in DNA but also by various sequence motifs of normal DNA that present challenges to replication. Towards a better understanding of the many determinants of genome stability, this chapter reviews the fidelity with which undamaged and damaged DNA is copied, with a focus on the eukaryotic B-and Y-family DNA polymerases, and considers how this fidelity is achieved.

Lesion processing: high-fidelity versus lesion-bypass DNA polymerases

“…Most Y-family DNA polymerases exhibit low processivity and a high error rate upon replicating normal, unmodified DNA [3,4]. The higher fidelity A-and B-family DNA polymerases have intrinsic error rates in the range of 10 −2 -10 −6 , whereas the error rates of lower fidelity Yfamily polymerases are in the 1-10 −3 range [59]. Specifically, the Y-family polymerase Dpo4 has a mismatch error rate of ~6.5 × 10 −3 and a single-base-deletion error rate of ~2.4 × 10 −3 [60], whereas the A-family polymerase BF has an error rate of ~1.5 × 10 −5 (http://www.freepatentsonline.com/5834253.html).…”

“…These interactions constitute a minor-groove scanning track or 'reading head' that enables the polymerase to sense an incorporated mismatch [31]; this proofreading promotes subsequent routing of the error-containing duplex for excision by an intrinsic exonuclease domain or an external exonuclease activity [10,59]. (Proofreading 3′→5′ exonuclease activity catalyzes the removal of mismatched nucleotides from the growing end of the primer strand.)…”

DNA polymerase zeta (pol ζ) in higher eukaryotes

“…Rev3 is a member of the B-family DNA polymerase family, which includes pols a, d and e [10]. It lacks a 3′ to 5′ exonuclease activity, and has relatively low fidelity [11]. Pol ζ is not essential for viability or genomic DNA replication in yeast.…”

Mouse models of DNA polymerases

“…Pol d is responsible for DNA synthesis on the lagging strand of DNA, while Pol e is responsible for DNA synthesis on the leading strand of DNA [Shcherbakova and Pavlov, 1996]. In addition to the polymerase activity, Pol d and Pol e possess 3 0 to 5 0 exonuclease activity, which enables them to proofread errors that may have occurred during DNA replication [Thomas et al, 1991;Uitto et al, 1992;McCulloch et al, 2008]. The exonuclease proofreading activity increases the fidelity of DNA synthesis thereby suppressing mutagenesis and preventing diseases such as cancer [Loeb, 2011].…”