DNA Recombination:- All Aspects of DNA Metabolism Come Together to Repair Stalled Replication Forks
Like all cells, bacteria sustain high levels of DNA dam age even under normal growth conditions. Most DNA
lesions are repaired rapidly by base-excision repair, nucleotide-excision repair, and the other pathways described earlier. Nevertheless, almost every bacterial replication fork encounters an unrepaired DNA lesion or break at some point in its journey from the replication origin to the terminus . DNA polymerase III cannot proceed past many types of DNA lesions, and these encounters tend to leave the lesion in a single-strand gap. An encounter with a DNA strand break creates a double-strand break. Both situations re quire recombinational DNA repair (Fig. 1). Under normal growth conditions, stalled replication forks are reactivated by an elaborate repair pathway encompassing recombinational DNA repair, the restart of replication, and the repair of any lesions left behind. All aspects of DNA metabolism come together in this process. After a replication fork has been halted, it can be restored by at least two major paths, both of which re quire the RecA protein. The repair pathway for lesion containing DNA gaps also requires the RecF, RecO, and RecR proteins. Repair of double-strand breaks requires the RecBCD enzyme (Fig. 1). Additional recombination steps are followed by a process called origin independent restart of replication, in which the replication fork reassembles with the aid of a complex of seven proteins (PriA, B, and C, and DnaB, C, G, and T). This complex, originally discovered as a component required for the replication of X174 DNA in vitro, is now termed the replication restart primosome. Restart of the replication fork also requires DNA polymerase II, in a role not yet defined; this polymerase II activity gives way to DNA polymerase III for the extensive replication generally required to complete the chromosome.
The repair of stalled replication forks entails a coordinated transition from replication to recombination and back to replication. The recombination steps function to fill the DNA gap or rejoin the broken DNA branch to recreate the branched DNA structure at the replication fork. Lesions left behind in what is now duplex DNA are repaired by pathways such as base-excision or nucleotide excision repair. Thus a wide range of enzymes encompassing every aspect of DNA metabolism ultimately take part in the repair of a stalled replication fork. This type of repair process is clearly a primary function of the ho mologous recombination system of every cell, and defects in recombinational DNA repair play an important role in human disease (Box 25–1).
FIGURE 1 Models for recombinational DNA repair of stalled replication forks. The replication fork collapses on encountering a DNA lesion (left) or strand break (right). Recombination enzymes pro mote the DNA strand transfers needed to repair the branched DNA structure at the replication fork. A lesion in a single-strand gap is re paired in a reaction requiring the RecF, RecO, and RecR proteins. Double-strand breaks are repaired in a pathway requiring the RecBCD enzyme. Both pathways require RecA. Recombination intermediates are processed by additional enzymes (e.g., RuvA, RuvB, and RuvC, which process Holliday intermediates). Lesions in double-stranded DNA are repaired by nucleotide-excision repair or other pathways. The replication fork re-forms with the aid of enzymes catalyzing origin-independent replication restart, and chromosomal replication is completed. The overall process requires an elaborate coordination of all aspects of bacterial DNA metabolism.
