Translesion synthesis in Escherichia coli: lessons from the NarI mutation hot spot.

Summary

Duplication of DNA containing damaged bases is a challenge to DNA polymerases that normally replicate with high speed, high accuracy and high processivity undamaged templates only. When a replicative DNA polymerase encounters a chemically altered base that it is unable to copy, a process called translesion synthesis (TLS) takes place during which the replicative polymerase is transiently replaced by a so-called specialized or lesion bypass polymerase. In addition to the central players that are the replicative and translesion DNA polymerases, TLS pathways involve accessory factors such as the general replication processivity factor (i.e. the beta-clamp in prokaryotes and PCNA in eukaryotes). In Escherichia coli, besides the beta-clamp, RecA plays a fundamental role as a co-factor of Pol V the major bypass polymerase in this organism. An integrated view of TLS pathways necessarily requires both genetic and biochemical studies. In this review we will attempt to summarize the insights into TLS gained over the last 25 years by studying a frameshift mutation hot spot, the NarI site. This site was initially discovered by serendipity when establishing a forward mutation spectrum induced by a chemical hepatocarcinogen, N-2-acetylaminofluorene (AAF). Indeed, this chemical carcinogen covalently binds to DNA forming adducts with guanine residues. When bound to G* in the NarI site, 5′-GGCG*CC-, AAF induces the loss of the G*pC dinucleotide at a frequency that is approximately 10(7)-fold higher than the spontaneous frequency. In vivo studies showed that the NarI mutation hot spot is neither restricted to the NarI sequence itself, nor to the carcinogen AAF. Instead, the hot spot requires a sequence containing at least two GpC repeats and any of a family of aromatic amides and nitro aromatic compounds that form a large class of human carcinogens. Genetic analysis initially revealed that the NarI frameshift pathway is SOS dependent but umuDC (i.e. Pol V) independent. More recently, DNA Pol II was identified as the enzyme responsible of this frameshift pathway. Concurrently the AAF adduct in the NarI site can be bypassed in an error-free way by Pol V. The NarI site thus offers a unique possibility to study the interplay between two specialized DNA polymerases, Pol II and Pol V, that can both extend replication intermediates formed when the replicative Pol III dissociates in the vicinity of the damage. Full reconstitution of the two pathways led us to highlight a key feature for TLS pathways, namely that it is critical the specialized DNA polymerase synthesizes, during the course of a single binding event, a patch of DNA synthesis (TLS patch) that is long enough as to “hide the lesion induced distortion” from the proofreading activity upon reloading of the replicative DNA polymerase (or any exonuclease that may get access to the primer when the specialized DNA polymerase detaches). The beta-clamp, to which all DNA polymerases bind, plays a critical role in allowing the specialized DNA polymerases to synthesize TLS patches that are long enough to resist such “external proofreading” activities.