Replication is required for the RecA localization response to DNA damage in Bacillus subtilis

Multiple Ku orthologues mediate DNA non-homologous end-joining in the free-living form and during chronic infection of Sinorhizobium meliloti

The bacterial non-homologous end-joining (NHEJ) apparatus is a two-component system that uses Ku and LigD to repair DNA double-strand breaks. Although the reaction mechanism has been extensively studied, much less is known about the physiological role of bacterial NHEJ. Recent studies suggest that NHEJ acts under conditions where DNA replication is reduced or absent (such as in a spore or stationary phase). Interestingly, genes encoding Ku and LigD have been identified in a wide range of bacteria that can chronically infect eukaryotic hosts. Strikingly, Sinohizobium meliloti, an intracellular symbiont of legume plants, carries four genes encoding Ku homologues (sku1 to sku4). Deletion analysis of the sku genes indicated that all Ku homologues are functional. One of these genes, sku2, is strongly expressed in free-living cells, as well as in bacteroid cells residing inside of the host plant. To visualize the NHEJ apparatus in vivo, SKu2 protein was fused to yellow fluorescent protein (YFP). Ionizing radiation (IR) induced focus formation of SKu2-YFP in free-living cells in a dosage-dependent manner. Moreover, SKu2-YFP foci formed in response to IR in non-dividing bacteroids, indicating that NHEJ system is functional even during the chronic infection phase of symbiosis.

Anticipating chromosomal replication fork arrest: SSB targets repair DNA helicases to active forks

In bacteria, several salvage responses to DNA replication arrest culminate in reassembly of the replisome on inactivated forks to resume replication. The PriA DNA helicase is a prominent trigger of this replication restart process, preceded in many cases by a repair and/or remodeling of the arrested fork, which can be performed by many specific proteins. The mechanisms that target these rescue effectors to damaged forks in the cell are unknown. We report that the single-stranded DNA binding (SSB) protein is the key factor that links PriA to active chromosomal replication forks in vivo. This targeting mechanism determines the efficiency by which PriA reaches its specific DNA-binding site in vitro and directs replication restart in vivo. The RecG and RecQ DNA helicases, which are involved in intricate replication reactivation pathways, also associate with the chromosomal replication forks by similarly interacting with SSB. These results identify SSB as a platform for linking a 'repair toolbox' with active replication forks, providing a first line of rescue responses to accidental arrest.

Paternal pronuclear DNA degradation is functionally linked to DNA replication in mouse oocytes

We recently demonstrated that mouse spermatozoa contain a mechanism to degrade their DNA into loop-sized fragments of about 50 kb, mediated by topoisomerase IIB, termed sperm chromatin fragmentation (SCF). SCF is often followed by a more complete digestion of the DNA with a sperm nuclease. When SCF-induced spermatozoa are injected into oocytes, the paternal pronuclei degrade their DNA after the initiation of DNA synthesis, but the maternal pronuclei are unaffected and replicate normally. Here, we tested whether the nuclease activity changes in spermatozoa of different maturation stages, and whether there is a functional relationship between the initiation of DNA synthesis and paternal DNA degradation induced by SCF in the zygote. We found that spermatozoa from the vas deferens have a much higher level of SCF activity than those from the cauda epididymis, suggesting that spermatozoa may acquire this activity in the vas deferens. Furthermore, paternal pronuclei formed in zygotes from injecting oocytes with SCF-induced vas deferens spermatozoa degraded their DNA, but this degradation could be inhibited by the DNA synthesis inhibitor, aphidicolin. Upon release from a 4 h aphidicolin-induced arrest, DNA synthesis was initiated in maternal pronuclei, while the paternal pronuclei degraded their DNA. Longer aphidicolin arrest resulted in the paternal pronuclei replicating their DNA, suggesting that delaying the initiation of DNA synthesis allowed the paternal pronuclei to overcome the SCF-induced DNA degradation pathway. These results suggest that the paternal DNA degradation, in oocytes fertilized with SCF-induced spermatozoa, is coupled to the initiation of DNA synthesis in newly fertilized zygotes.

Nutritional control of elongation of DNA replication by (p)ppGpp

DNA replication is highly regulated in most organisms. Although much research has focused on mechanisms that regulate initiation of replication, mechanisms that regulate elongation of replication are less well understood. We characterized a mechanism that regulates replication elongation in the bacterium Bacillus subtilis. Replication elongation was inhibited within minutes after amino acid starvation, regardless of where the replication forks were located on the chromosome. We found that small nucleotides ppGpp and pppGpp, which are induced upon starvation, appeared to inhibit replication directly by inhibiting primase, an essential component of the replication machinery. The replication forks arrested with (p)ppGpp did not recruit the recombination protein RecA, indicating that the forks are not disrupted. (p)ppGpp appear to be part of a surveillance mechanism that links nutrient availability to replication by rapidly inhibiting replication in starved cells, thereby preventing replication-fork disruption. This control may be important for cells to maintain genomic integrity.