The idea of two-strand repair. (A) A DNA molecule with a two-strand lesion (small open rectangles in the solid duplex) is shown side-by-side with an intact homolog (open duplex). (B) The two sequences have exchanged strands in a homologous region, converting the two-strand lesion into a pair of one-strand lesions. (C) Junction resolution (the strands to cut are shown in panel B) separates the chromosomes from each other. (D) Excision repair removes the one-strand lesions, completing the overall repair reaction. Note that if black and white “parental” DNAs are not identical, the resulting chromosomes may become “recombinant.”

The four ways to resolve a joint molecule with a double junction. Lowercase letters w, x, y, and z designate unique sites which serve as markers on the homologous chromosomes. A junction is resolved by two symmetrical single-strand cuts (small black arrows in panel B) across each other. Each such diagonal pair of cuts is numbered either 1 or 2 for each junction. If junctions freely isomerize and are resolved independently of each other, four outcomes of the resolution are expected. In two of the outcomes, the chromosome arms will be exchanged, resulting in recombinant chromosomes. (A) A joint molecule with two junctions as shown in Fig. 1B. (B) The same joint molecule isomerized to show both junctions in the open planar configuration (498). (C) The four resolution outcomes, numbered according to the resolution options realized at the left and the right junctions.

The two major types of replication-induced two-strand lesions. A replication fork moves from left to right along the template DNA with unrepaired one-strand lesions. The left template contains a noncoding lesion (T=T, thymine dimer), the right template has a single-strand interruption. Additional explanations are given in the figure and in the text.

The two pathways of recombinational repair in E. coli. On the left, the RecF (daughter strand gap repair) pathway is shown; on the right, the RecBC (double-strand end repair) pathway is shown. Additional explanations are given in the text.

An idealized induction kinetics of the four groups of LexA-controlled genes (also, see reference 611). The graph illustrates the well-regulated nature of the SOS response. Both the x axis (time) and y axis (the level of the SOS induction) are in arbitrary units; therefore, the heights of the three curves are not to be compared.

RecA filament in vitro: photographs and molecular model. (A) A relaxed circular duplex DNA completely covered by RecA filament. Naked duplex DNA of the same length, lying mostly inside the RecA filament, illustrates that DNA within RecA filament is stretched 1.5 times. Reprinted from reference 625 with permission of the publisher. (B) A RecA-covered circular ssDNA molecule; the arrow points to a segment complexed by SSB. Below, another ssDNA circle of the same length can be seen, but since it is entirely complexed with SSB, it appears very different, i.e., much smaller and kinky. Note that while RecA filament stretches ssDNA, SSB compacts it. Reprinted from reference 246 with permission of the publisher. (C) A crystal structure-based molecular model of an 18-monomer segment of RecA filament with three symmetry-related monomers in gray. Each of these monomers is enlarged on the right to show residues conserved among eubacterial RecA proteins (see reference 524 for details). In such a filament, the 5′ end of DNA1 would be at the top. Reprinted from reference 524 with permission of the publisher.

The distinguishable phases of RecA-promoted reactions, as they are thought to happen in vivo. Black lines indicate a damaged duplex; white lines indicate an intact duplex; the open rectangle with rounded corners indicates a RecA filament; the irregularity in one of the black DNA strands indicates a noncoding lesion. The left side represents daughter strand gap repair; the right side represents double-strand end repair. Explanations are given in the figure.

SSB helps in the assembly of the functional RecA filament. The thick line indicates ssDNA; stem-loop structures indicate secondary (duplex) structures in ssDNA at physiological Mg²⁺ concentrations; open rectangles with rounded corners indicate RecA filaments; quartets of small circles indicate SSB tetramers. Without SSB (the top and the left side), formation of long contiguous RecA filaments on ssDNA is compromised because the growth of nascent filaments is impossible past the secondary structures. SSB helps RecA to polymerize into long contiguous filaments (the right side and the bottom) by ironing out secondary structures in the ssDNA.

The three ways to remove a double DNA junction. A pair of four-strand junctions is shown, but the same applies to a pair of three-strand junctions or to a combination of one four-strand junction and one three-strand junction. The two DNA duplexes participating in the joint molecule are shown as either solid or open double lines. Small arrows near the junctions indicate the direction of junction translocation. Scissors mark the position of strand cuts. (A) Removal by translocation only (topoisomerase model). (B) Removal by symmetrical single-strand cuts only (resolution). (C) Removal by a combination of cuts and translocation. Additional explanations are given in the text.

Removal of a single DNA junction. A three-strand junction is shown, but the same applies to a four-strand junction. The two DNA duplexes participating in the joint molecule are shown as either solid or open double lines. Small arrows near the junctions indicate the direction of junction translocation. Scissors mark the position of strand cuts. (A) Removal by translocation only. (B) Removal by symmetric single-strand cuts only. Note that for the three-strand junction, the black strand already has an end across the cut in the white strand. (C) Removal by a combination of a cut and translocation. Additional explanations are given in the text. The last two options create a replication fork framework, whereas the first option seems to be nonproductive. However, if the original two-strand lesion was a double-strand break and the invading end has already been extended by DNA synthesis, the expelled extended end can now anneal with the other end of the break, permitting lesion repair (517).

Interactions of RuvA, RuvB, and RuvC with Holliday junctions. The two homologous duplexes (solid and open double lines) are connected by a single Holliday junction. RuvA tetramer is shown as the four-petal flower, RuvB hexameric rings are shown as the trapezoid washers on DNA duplexes, RuvC dimer (E) is shown as the pair of open circles. The direction of DNA movement through RuvAB complex in panels D and E is indicated by arrows. (A) A Holliday junction in a folded conformation, observed in vitro under conditions mimicking physiological ones. (B) A RuvA tetramer binds the junction to open it into a square planar conformation, while two RuvB hexamers bind two opposite arms of the junction. (C) The RuvAB translocase: the same as in panel B, but the second RuvA tetramer binds to the unoccupied side of the junction, locking it in a turtle shell configuration. (D) One of the RuvA tetramers is removed to show junction isomerization, promoted by the pulling action of RuvB (compare with panel B). (E) RuvABC resolvasome: one of the RuvA tetramers has left to allow a RuvC dimer to assume a position for the junction resolution. The resolution sites (diamonds in the opposite DNA strands) are drawn into the junction by the action of RuvB. (F) RuvC cleavage at the resolution sites separates the interacting homologs. The RuvABC resolvasome is not shown.

The “flip” and “flop” sides of a Holliday junction in the open conformation. The same junction is shown from the opposite sides. The 3′ and 5′ ends of DNA strands are marked. In the center, the 5′-to-3′ direction around the junctions is indicated by arrows. RuvC binds to the “clockwise” side of the junction, whereas RuvA binds to the “counterclockwise” side.

Hypothetical removal of a single three-strand junction by RecG. RecA filament is shown as an open rectangle with rounded corners; RecA monomers (in panel C) are shown as open circles; RecG is shown as a dotted oval. The small arrow in panel A indicates the position of the required single-strand incision. Explanations are given in the text.

Experimentally established principles of the daughter strand gap repair in E. coli. Solid lines indicate parental DNA strands; open lines indicate newly synthesized daughter DNA strands; diamonds indicate thymine dimers; small horizontal arrows indicate single-strand scissions required to resolve the joint molecules. (A) A DNA molecule containing unrepaired noncoding lesions (for example, thymine dimers). (B) Replication of this molecule generates two molecules with single-strand gaps in the daughter strands opposite the lesions (538). Eventually, these gaps are repaired in a RecA-dependent way (606). (C to H) Experiments by Rupp et al. (539) had revealed that after gap closure, the newly synthesized strands are connected with the parental strands (strand exchange), suggesting a model for recombinational repair of daughter-strand gaps (C to E). Later, Ley (357) found that the gaps are transferred from the daughter strands to the parental strands, while Ganesan (199) found that the thymine dimers are transferred in the opposite direction, from the parental strands to the daughter strands, suggesting the formation and resolution of Holliday junctions (F to H).

Overview of daughter strand gap repair. (A) A DNA molecule with a daughter-strand gap. T=T, the thymine dimer that caused the gap. (B) Synapsis of the gapped molecule with the intact homologous DNA. (C) Filling in of the gap and repair of the lesion that caused the gap. (D) Disengagement of the two DNA molecules. The RuvC cleavages are indicated by small vertical arrows in panel C. Additional explanations are given in the text and in the figure.

Presynaptic phase of the daughter-strand gap repair: RecA filament assembly and replisome reactivation. The replisome is depicted as a big open oval, and its DnaN subunit (the clamp) is indicated as a smaller open rectangle with rounded corners. The 3′ end of the nascent DNA is stalled at the noncoding lesion (the irregularity in the lower strand). SSB is shown as quartets of open circles around single-stranded region; RecFR (small black rectangles) are associated with the RNA primer (wavy segment in the upper strand at the very right). The RecA filament is shown as a hatched rectangle with rounded corners spreading to the left. Explanations are given in the figure and in the text.

Topoisomerase requirements during synapsis. Regular DNA superhelicity is shown in the top and bottom double helices. In the two middle panels, the helices are either overwound (too much coiling) or underwound (missing coils). DNA gyrase removes extra coils from the original (black-black) duplex, while DNA Topo I (TopA) introduces the missing coils in the hybrid (black-white) duplex.

Synaptic and postsynaptic phases of daughter strand gap repair. This figure is a sequel to Fig. 16. The RecA filament is shown as a hatched rectangle with rounded corners. From top to bottom, the stages are pairing with an intact homolog, repair of the gap, and removal of the DNA junctions and the associated RecA filament. Explanations are given in the figure and in the text.

Model for the translesion DNA synthesis. This figure is a sequel to Fig. 16 and shows an alternative to the mechanism illustrated in Fig. 18. The RecA filament is shown as a hatched rectangle; the DnaN clamp is shown as a small open rectangle; UmuC is shown as a small black rectangle associated with the DnaN clamp; UmuD is shown as small black dimer circles, some of them associated with UmuC; the replisome is shown as an open oval. Explanations are given in the figure and in the text.

Replication-dependent origin of double-strand ends. (A) Replication fork collapse at a single-strand interruption in template DNA. The replisome is shown as the square group of circles, speeding from left to right along the DNA while replicating it. (B) Preexisting interruptions in the same DNA strand at both replication forks of a replication bubble cause chromosome fragmentation.