**3. Mechanisms of DNA recombinational repair known in model bacteria**

Although the bulk of DNA damage affects one strand of a duplex DNA segment, occasionally both DNA strands opposite each other are damaged; the latter situation necessitates recombinational repair using an intact homologous DNA sequence [56, 57]. DNA double-strand breaks (DSB) occur as a result of a variety of physical or chemical insults that modify the DNA (e.g. DNA strands cross-links). In addition, if a replication fork meets damaged bases that cannot be replicated, the fork can collapse leading to a DSB. In *E. coli*, 20-50% of replication forks require recombinational repair to overcome damage [58].

Homologous recombinational repair requires a large number of proteins that act at various stages of the process [56]. The first stage, **pre-synapsis**, is the generation of 3' singlestranded (ss) DNA ends that can then be used for annealing with the homologous sequence on the sister chromosome. In *E. coli*, the two types of two-strand lesions (double strand end and daughter strand gap) are repaired by two separate pathways, RecBCD and RecFOR, respectively [57]. The second and most crucial step in DNA recombination is the introduction of the 3' DNA overhang into the homologous duplex of the sister chromosome, termed **synapsis**. This is performed by RecA in bacteria. RecA binds to ssDNA in an ATPdependent manner, and RecA-bound ssDNA (in a right-handed helix structure) can invade homologous duplex DNA and mediate strand annealing, accompanied by extrusion of the other strand that can pair with the remaining 5' overhang of the DSB (called D-loop formation).

During DNA recombination, the single stranded DNA (ssDNA) is always coated (protected) by ssDNA-binding protein (SSB), which has a higher affinity to ssDNA than RecA. RecA needs to be loaded (during pre-synapsis stage), either by RecBCD or RecFOR, onto the generated ssDNA that is coated with SSB. During the third step in recombination, **postsynapsis**, RecA-promoted strand transfer produces a four-stranded exchange, or Holliday junctions (HJ) [59]. The RecG and RuvAB helicases are two pathways that process the branch migration of HJ. Finally, RuvC resolves HJ in an orientation determined by RuvB, and the remaining nicks are sealed by DNA ligase.

Several other genes (recJ, recQ, recN) are also required for recombination, although their functions are unclear [60, 61]. Single stranded exonuclease RecJ and RecQ helicase are sometimes needed to enlarge the gap for RecFOR to act [62]. RecN, RecO, and RecF were found to be localized to distinct foci on the DNA in *Bacillus subtilis* cells after induction of DSBs [63]. These proteins form active repair centers at DSBs and recruit RecA, initiating

of DNA damage is not understood. No DNA repair genes, a hallmark of the SOS response, were induced in either the antibiotic-treated cells or the recombination gene deleted strain. Surprisingly, several genes involved in natural competence for DNA transformation (*com* T4SS components *comB3*, *comB4* and *comB9*) were induced significantly. Indeed, natural transformation frequency was shown to be increased under DNA damage conditions. Another DNA damage-induced gene was a lysozyme-encoding gene. Experimental evidence was provided that a DNA damage-induced lysozyme may target susceptible cells in culture and provide a source of DNA for uptake [55]. Taken together, DNA damage (mainly DSBs in their experiments) induces the capacity for taking up DNA segments from the neighboring cells of the same strain (homologous) or co-colonizing strain (homeologous)

**3. Mechanisms of DNA recombinational repair known in model bacteria** 

Although the bulk of DNA damage affects one strand of a duplex DNA segment, occasionally both DNA strands opposite each other are damaged; the latter situation necessitates recombinational repair using an intact homologous DNA sequence [56, 57]. DNA double-strand breaks (DSB) occur as a result of a variety of physical or chemical insults that modify the DNA (e.g. DNA strands cross-links). In addition, if a replication fork meets damaged bases that cannot be replicated, the fork can collapse leading to a DSB. In *E. coli*, 20-50% of replication forks require recombinational repair to overcome

Homologous recombinational repair requires a large number of proteins that act at various stages of the process [56]. The first stage, **pre-synapsis**, is the generation of 3' singlestranded (ss) DNA ends that can then be used for annealing with the homologous sequence on the sister chromosome. In *E. coli*, the two types of two-strand lesions (double strand end and daughter strand gap) are repaired by two separate pathways, RecBCD and RecFOR, respectively [57]. The second and most crucial step in DNA recombination is the introduction of the 3' DNA overhang into the homologous duplex of the sister chromosome, termed **synapsis**. This is performed by RecA in bacteria. RecA binds to ssDNA in an ATPdependent manner, and RecA-bound ssDNA (in a right-handed helix structure) can invade homologous duplex DNA and mediate strand annealing, accompanied by extrusion of the other strand that can pair with the remaining 5' overhang of the DSB (called D-loop

During DNA recombination, the single stranded DNA (ssDNA) is always coated (protected) by ssDNA-binding protein (SSB), which has a higher affinity to ssDNA than RecA. RecA needs to be loaded (during pre-synapsis stage), either by RecBCD or RecFOR, onto the generated ssDNA that is coated with SSB. During the third step in recombination, **postsynapsis**, RecA-promoted strand transfer produces a four-stranded exchange, or Holliday junctions (HJ) [59]. The RecG and RuvAB helicases are two pathways that process the branch migration of HJ. Finally, RuvC resolves HJ in an orientation determined by RuvB,

Several other genes (recJ, recQ, recN) are also required for recombination, although their functions are unclear [60, 61]. Single stranded exonuclease RecJ and RecQ helicase are sometimes needed to enlarge the gap for RecFOR to act [62]. RecN, RecO, and RecF were found to be localized to distinct foci on the DNA in *Bacillus subtilis* cells after induction of DSBs [63]. These proteins form active repair centers at DSBs and recruit RecA, initiating

that may be used for recombinational DNA repair.

and the remaining nicks are sealed by DNA ligase.

damage [58].

formation).

homologous recombination. RecN was shown to play an important role in repairing DSBs, probably coordinating alignment of the broken segments with intact duplexes to facilitate recombination [64].
