Low-fidelity DNA synthesis by human DNA polymerase theta

Abstract

Human DNA polymerase theta (pol θ or POLQ) is a proofreading-deficient family A enzyme implicated in translesion synthesis (TLS) and perhaps in somatic hypermutation (SHM) of immunoglobulin genes. These proposed functions and kinetic studies imply that pol θ may synthesize DNA with low fidelity. Here, we show that when copying undamaged DNA, pol θ generates single base errors at rates 10- to more than 100-fold higher than for other family A members. Pol θ adds single nucleotides to homopolymeric runs at particularly high rates, exceeding 1% in certain sequence contexts, and generates single base substitutions at an average rate of 2.4 × 10−3, comparable to inaccurate family Y human pol κ (5.8 × 10−3) also implicated in TLS. Like pol κ, pol θ is processive, implying that it may be tightly regulated to avoid deleterious mutagenesis. Pol θ also generates certain base substitutions at high rates within sequence contexts similar to those inferred to be copied by pol θ during SHM of immunoglobulin genes in mice. Thus, pol θ is an exception among family A polymerases, and its low fidelity is consistent with its proposed roles in TLS and SHM.

DNA polymerase from temperate phage Bam35 is endowed with processive polymerization and abasic sites translesion synthesis capacity

“…Similar analyses with other polymerases have shown that error rates are usually much higher for substitutions than for insertion/ deletions (InDels, 4), except in the case of A-family human DNA polymerase θ (POLQ) (36,37), which has a higher error rate than replicative polymerases (on the order of 10 −3 -10 −4 ), owing mainly to nucleotide insertions (3.3 × 10 −3 ) and deletions (1.4 × 10 −3 ), particularly in homopolymeric DNA tracks. InDels are the signature for misaligned primer templates containing an extra base in the template strand (for deletions) or in the primer strand (for additions), stabilized by a number of correct base pairs that separate the extra base from the primer end at the catalytic site (38).…”

Measurements of spontaneous rates of mutations in the recent past and the near future

“…20) and of context dependence, the influence of the nucleotide state of neighbouring sites (Gordenin & Resnick 1998;Kondrashov & Rogozin 2004;Kondrashov et al 2006;Hodgkinson et al 2009). Different polymerases can lead to different patterns of mutation (Pavlov et al 2006;Arana et al 2008) and their function also causes the mutagenic effects of methylation (Holliday & Grigg 1993) and mutational hotpots (Rogozin & Pavlov 2003). We also have some estimates of the relative rates of indels (Petrov et al 2000;Yang et al 2001a,b;Denver et al 2004;Haag-Liautard et al 2007), transposon insertions (Nuzhdin & Mackay 1994) and strand biases in the mitochondrial (Tanaka & Ozawa 1994), nuclear and prokaryotic genomes (Green et al 2003;Morton & Morton 2007;Unniraman & Schatz 2007).…”

A Polymerase Tautomeric Model for Radiation Induced Bystander Effects: A Model for Untargeted Base Substitution Mutagenesis during Error Prone and SOS Replication of Double Stranded DNA Containing Thymine and Adenine in Rare Tautomeric Forms

“…Many specialized DNA polymerases can lead translesion synthesis opposite of cyclobutane pyrimidine dimers [23,31,35,[40][41][42][43][44] and participate in the formation of untargeted mutations. For example, the DNA polymerase pol θ is processivity polymerase, which implies that it can strongly regulated to avoid mutagenesis [41].…”

“…For example, the DNA polymerase pol θ is processivity polymerase, which implies that it can strongly regulated to avoid mutagenesis [41]. Error-prone polymerases V Escherichia coli (Pol V) and polymerase IV (Pol IV) are responsible for SOSinduced untargeted mutations [23,35,42].…”

“…The role of the polymerases in cancer is investigated [59,60]. However, despite the obvious advances in the study of the structure and functions of polymerases [19,20,37,[39][40][41][45][46][47][48][49][50][51][52][53][54][55] the modern theory of mutagenesis, based on polymerase paradigm, cannot fully explain many phenomena of mutagenesis. These include the reasons for the formation of hot and cold spots of ultraviolet mutagenesis [61,62].…”