14. Error-prone repair and mutator phenotypes

14.14 Error-prone repair and mutator phenotypes

The existence of repair systems that engage in DNA synthesis raises the question of whether their quality control is comparable with that of DNA replication. So far as we know, most systems, including uvr-controlled excision repair, do not differ significantly from DNA replication in the frequency of mistakes. However, error-prone synthesis of DNA occurs in E. coli under certain circumstances.

The error-prone feature was first observed when it was found that the repair of damaged λ phage DNA is accompanied by the induction of mutations if the phage is introduced into cells that had previously been irradiated with UV. This suggests that the UV irradiation of the host has activated functions that generate mutations. The mutagenic response also operates on the bacterial host DNA.

What is the actual error-prone activity? It is a DNA polymerase that inserts incorrect bases, which represent mutations, when it passses any site at which it cannot insert complementary base pairs in the daughter strand. Functions involved in this error-prone pathway are identified by mutations in the genes umuD and umuC, which abolish UV-induced mutagenesis. This implies that the UmuC and UmuD proteins cause mutations to occur after mutagenesis by UV. The genes constitute the umuDC operon, whose expression is induced by DNA damage. Their products form a complex UmuD′₂C, consisting of two subunits of a truncated UmuD protein and one subunit of UmuC. UmuD is cleaved by RecA, which is activated by DNA damage (see 14.17 RecA triggers the SOS system).

The UmuD′₂C complex has DNA polymerase activity. It is called DNA polymerase V, and is responsible for synthesizing new DNA to replace sequences that have been damaged by UV (Maor-Shoshani et al., 2000). This is the only enzyme in E. coli that can bypass the classic pyrimidine dimers produced by UV. The polymerase activity is "error-prone". Mutation of umuC or umuD inactivates the enzyme, which explains why UV no longer induces mutations (for review see Goodman and Tippin, 2000). Some plasmids carry genes called mucA and mucB, which are homologs of umuD and umuC, and whose introduction into a bacterium increases resistance to UV killing and susceptibility to mutagenesis.

How does an alternative DNA polymerase get access to the DNA? When the replicase (DNA polymerase III) encounters a block, such as a thymidine dimer, it stalls. Then it is displaced from the replication fork and replaced by DNA polymerase V. In fact, DNA polymerase V uses some of the same ancillary proteins as DNA polymerase III. The same situation is true for DNA polymerase IV, the product of dinB, which is another enzyme that acts on damaged DNA (Wagner et al., 1999). DNA polymerases IV and V are part of a larger family, including eukaryotic DNA polymerases, that are involved in repairing damaged DNA (see 14.18 Eukaryotic repair systems) (for review see Friedberg, Feaver, and Gerlach, 2000).

Genes whose products are involved in controlling the fidelity of DNA synthesis during either replication or repair may be identified by mutations that have a mutator phenotype. A mutator mutant has an increased frequency of spontaneous mutation. If identified originally by the mutator phenotype, a gene is described as mut; but often a mut gene is later found to be equivalent with a known replication or repair activity.

The general types of activities are identified by mut genes fall into groups. The major group consists of components of mismatch-repair systems. They include the dam methylase that identifies the target for repair (see next section) and enzymes that participate directly or indirectly in the removal of particular types of damage (mutH,U,S,L,Y); failure to remove a damaged or mispaired base before replication allows it to induce a mutation. A smaller group, typified by dnaQ, is concerned with the accuracy of synthesizing new DNA.

This section updated 9-27-2000

Reviews

Goodman, M. F. and Tippin, B. (2000). Sloppier copier DNA polymerases involved in genome repair.. Curr. Biol. 10, 162-168.

Research

Friedberg, E. C. , Feaver, W. J. , and Gerlach, V. L. (2000). The many faces of DNA polymerases: strategies for mutagenesis and for mutational avoidance. Proc. Nat. Acad. Sci. USA 97, 5681-5683.

Maor-Shoshani, A. , Reuven, N. B. , Tomer, G. , and Livneh, Z. (2000). Highly mutagenic replication by DNA polymerase V (UmuC) provides a mechanistic basis for SOS untargeted mutagenesis.. Proc. Nat. Acad. Sci. USA 97, 565-570.

Wagner, J. , Gruz, P. , Kim, S. R. , Yamada, M. , Matsui, K. , Fuchs, R. P. , and Nohmi, T. (1999). The dinB gene encodes a novel E. coli DNA polymerase, DNA pol IV, involved in mutagenesis.. Mol. Cell 4, 281-286.