Genes VII

Excision repair systems vary in their specificity, but share the same general features. Each system removes mispaired or damaged bases from DNA and then synthesizes a new stretch of DNA to replace them. The main type of pathway for excision repair is illustrated in Figure 14.27.

In the incision step, the damaged structure is recognized by an endonuclease that cleaves the DNA strand on both sides of the damage.

In the excision step, a 5′ V3′ exonuclease removes a stretch of the damaged strand.

In the synthesis step, the resulting single-stranded region serves as a template for a DNA polymerase to synthesize a replacement for the excised sequence. (Synthesis of the new strand could be associated with removal of the old strand, in one coordinated action.) Finally, DNA ligase covalently links the 3′ end of the new material to the old material.

Different excision repair modes are identified by the heterogeneity of the lengths of the segments of repaired DNA. These pathways are described as very short patch repair (VSP), short patch repair, and long patch repair. The VSP system deals with mismatches between specific bases (see later). The latter two excision repair systems both involve the uvr genes.

The uvr system of excision repair includes three genes, uvrA,B,C, that code for the components of a repair endonuclease. It functions in the stages indicated in Figure 14.28. First, a UvrAB combination recognizes pyrimidine dimers and other bulky lesions. Then UvrA dissociates (this requires ATP), and UvrC joins UvrB. The UvrBC combination makes an incision on each side, one 7 nucleotides from the 5′ side of the damaged site, and the other 3 V4 nucleotides away from the 3′ side. This also requires ATP. UvrD is a helicase that helps to unwind the DNA to allow release of the single strand between the two cuts. The enzyme that excises the damaged strand is probably DNA polymerase I. The events are basically the same, although their order is different, in the eukaryotic repair pathway shown in Figure 14.37.

The average length of excised DNA is ~12 nucleotides, which gives rise to the description of this mode as the short-patch repair. The enzyme involved in the repair synthesis probably also is DNA polymerase I (although DNA polymerases II and III can substitute for it).

For bulky lesions, short-patch repair accounts for 99% of the excision repair events. The remaining 1% involve the replacement of stretches of DNA mostly ~1500 nucleotides long, but extending up to >9000 nucleotides. This mode also requires the uvr genes and involves DNA polymerase I. A difference between the two modes of repair is that short Vpatch repair is a constitutive function of the bacterial cell, but long-patch repair must be induced by damage (see later). Long-patch repair probably acts on lesions found in regions near replication forks. We have not yet characterized the differences between these modes in terms of the involvement of different gene products.