A single hydrophobic cleft in the Escherichia coli processivity clamp is sufficient to support cell viability and DNA damage-induced mutagenesis in vivo

A mutant E. coli β clamp protein lacking a functional hydrophobic cleft (βC) complemented the temperature sensitive growth phenotype of a strain bearing the dnaN159 allele, which encodes a thermolabile mutant clamp protein (β159). Complementation was conferred by a βC/β159 heterodimer, and was observed only in the absence of the dinB gene, which encodes DNA polymerase IV (Pol IV). Furthermore, the complemented strain was proficient for umuDC (Pol V) -dependent ultraviolet light (UV) -induced mutagenesis.Our results suggest that a single cleft in the homodimeric E. coli β sliding clamp protein is sufficient to support both cell viability, as well as Pol III, Pol IV, and Pol V function in vivo. These findings provide further support for a model in which different Pols switch places with each other on DNA using a single cleft in the clamp.Viability of all organisms depends upon a capacity to both accurately repair damaged DNA, as well as tolerate DNA lesions that for whatever reason evade repair [1]. In contrast to repair, which acts to either directly reverse the damage, or to excise modified bases so that the affected sequence may be re-synthesized, DNA damage tolerance mechanisms act to enable replication past the damaged site, without catalyzing repair of the lesion(s). Generally speaking, DNA damage tolerance mechanisms fall into one of two broad classes: (i) daughter strand switching, which refers to a collection of recombinational mechanisms that act to physically restructure the DNA at the replication fork to enable the complementary daughter strand to act as template to support replication beyond the damaged site(s) [1,2]; and (ii) translesion DNA synthesis (TLS), which refers to the process by which one or more specialized DNA polymerases (Pols) are recruited to catalyze replication past damaged sites in the DNA [3]. Since most Pols capable of catalyzing TLS display remarkably low fidelity on undamaged DNA, their actions must be very tightly controlled in viv