Motif A of bacteriophage T4 DNA polymerase: role in primer extension and DNA replication fidelity. Isolation of new antimutator and mutator DNA polymerases

Using 2-aminopurine fluorescence and mutational analysis to demonstrate an active role of bacteriophage T4 DNA polymerase in strand separation required for 3' --> 5'-exonuclease activity

The fluorescence of 2-aminopurine deoxynucleotide positioned in a 3'-terminal mismatch was used to evaluate the pre-steady state kinetics of the 3' --> 5' exonuclease activity of bacteriophage T4 DNA polymerase on defined DNA substrates. DNA substrates with one, two, or three preformed terminal mispairs simulated increasing degrees of strand separation at a primer terminus. The effects of base pair stability and local DNA sequence on excision rates were investigated by using DNA substrates that were either relatively G + C- or A + T-rich. The importance of strand separation as a prerequisite to the hydrolysis of a terminal nucleotide was demonstrated by using a unique mutant DNA polymerase that could degrade single-stranded but not double-stranded DNA, unless two or more 3'-terminal nucleotides were unpaired. Our results led us to conclude that the reduced exonuclease activity of this mutant DNA polymerase on duplex DNA substrates is due to a defect in melting the primer terminus in preparation for the excision reaction. The mutated amino acid (serine substitution for glycine at codon 255) resides in a critical loop structure determined from a crystallographic study of an amino-terminal fragment of T4 DNA polymerase. These results suggest an active role for amino acid residues in the exonuclease domain of the T4 DNA polymerase in the strand separation step.

Replication of O6-methylguanine-containing DNA by repair and replicative DNA polymerases

The biological consequences of O6-methylguanine (m6G) in DNA are well recognized. When template m6G is encountered by DNA polymerases, replication is hindered and trans-lesion replication results in the preferential incorporation of dTMP opposite template m6G. Thus, unrepaired m6G in DNA is both cytotoxic and mutagenic. Yet, cell lines tolerant to m6G in DNA have been isolated, which indicates that some cellular DNA polymerases may replicate m6G-containing DNA with reasonable efficiency. Previous reports suggested that mammalian pol beta could not replicate m6G-containing DNA, but we find that pol beta can catalyze trans-lesion replication; however, the lesion must reside in the optimal context for pol beta activity, single- or short nucleotide gapped substrates. Primed single-stranded DNA templates, with or without template m6G, were poor substrates for pol beta as reported in earlier studies. In contrast, trans-lesion replication by bacteriophage T4 DNA polymerase was observed for primed single-stranded DNA templates. Replication of m6G-containing DNA by T4 DNA polymerase required the gp45 accessory protein that clamps the polymerase to the DNA template. The rate-limiting step in replicating m6G-containing DNAs by both DNA polymerases tested was incorporation of dTMP across from the lesion.

Suppressors of Escherichia coli mutT: antimutators for DNA replication errors

Previous studies in our laboratory used a papillation assay to identify a set of mutations in the E. coli dnaE gene that confer increased accuracy of DNA replication (antimutators). These antimutators were isolated as suppressors of the hugh mutability of a mismatch-repair-defective mutL strain, in which the majority of mutations represent uncorrected replication errors (mainly A.T --> G.C and G.C --> A.T transitions). In the present study, we have sought suppressors of the high mutability of a mutT mutator strain. mutT strains produce a high frequency of A.T --> C.G transversions due to their lack of the mutT-encoded 8-oxo-dGTPase, leading to a high frequency of A.(8-oxoG) mispairing errors. Following localized mutagenesis of the dnaE-dnaQ region of the chromosome, two strong suppressors of mutT mutability were obtained, both residing in the dnaE gene (dnaE940 and dnaE941). When subsequently tested in a mutL strain, these two alleles also proved antimutators in this background, dnaE941 being significantly stronger than the previously isolated antimutators. The results suggest that the DNA polymerase may use similar mechanisms to discriminate against A.(8-oxoG) transversion mispairs and A.C or T.G transition mispairs. The finding may also have significance for teh interpretation of the antimutator effect conferred by these dnaE alleles in a wild-type (mut+) background.

Selection of bacteriophage T4 antimutator DNA polymerases: a link between proofreading and sensitivity to phosphonoacetic acid

During DNA replication, DNA polymerases alternate between DNA synthesis and proofreading the newly synthesized DNA. In order to understand the molecular details of how DNA polymerases determine the balance between polymerase and proofreading activities, it would be useful to have mutants which switch between the two activities either more or less frequently. Antimutator DNA polymerases switch more frequently and thus have more opportunity for proofreading. We have observed that mutant DNA polymerases which proofread less frequently have a mutator phenotype and are inhibited by the pyrophosphate analogue phosphonoacetic acid. Sensitivity to phosphonoacetic acid can be used to isolate second-site suppressor mutations. These suppressor mutations encode amino acid substitutions which produce antimutator DNA polymerases.

Isolation and characterization of ten mutator alleles of the mitochondrial DNA polymerase-encoding MIP1 gene from Saccharomyces cerevisiae

Ten mutator alleles of MIP1, the gene encoding mitochondrial (mt) DNA polymerase, have been isolated after in vitro random mutagenesis. Five mutations causing a 100-400-fold increase in the frequency of erythromycin-resistant (ErR) mt mutants in yeast mapped to the 3'-5' exonuclease (Exo) domain, and mainly to the three conserved motifs Exo1, Exo2 and Exo3 of this domain, highlighting the importance of proofreading in accurate mt DNA replication. The essential role of the invariant glutamate at the Exo1 site was confirmed and the participation of four amino acids (aa) in the 3'-5' Exo function revealed. Another mutation that is located between the Exo1 and Exo2 sites produced an extremely strong mutator phenotype associated with impaired DNA replication, but could be assigned neither to a conserved aa nor to a conserved portion of the 3'-5' exonuclease domain. The importance of the polymerization domain in accurate mt DNA replication was pointed out by three mutator mutations. Two of these severely impaired mt DNA replication and were assigned to a subdomain of the polymerase which probably corresponds to the 'fingers' module of the Klenow (large) fragment of Escherichia coli DNA polymerase I (PolIk). The third, which did not alter the efficiency of DNA replication, was located at the active center of the polymerization reaction. Finally, the mutation, R1001I, mapped to the C-terminal part of the MIP1 protein which has no counterpart in prokaryotic DNA polymerases.

Use of genetic analyses to probe structure, function, and dynamics of bacteriophage T4 DNA polymerase

Functionally distinct mutant DNA polymerases have been isolated by the genetic selection strategies described here. These methods can be supplemented by the use of targeted mutagenesis procedures to enhance mutagenesis of DNA polymerase genes and to direct mutagenesis to specific sites in cloned DNA polymerases (see [22-24, 28], this volume). The power of genetic selection is in the ability to identify amino acid residues that are critical for protein structure and function that may not be obvious from studies of structural data alone. For the study of DNA polymerases, it is essential to identify residues involved in the movement of the DNA polymerase along the DNA template and in shuttling the DNA between the polymerase and exonuclease active centers. Ongoing studies are directed toward these goals.