Characterisation of RuvAB-Holliday junction complexes by glycerol gradient sedimentation

Holliday junction branch migration driven by AAA+ ATPase motors

Holliday junctions are key intermediate DNA structures during genetic recombination. One of the first Holliday junction-processing protein complexes to be discovered was the well conserved RuvAB branch migration complex present in bacteria that mediates an ATP-dependent movement of the Holliday junction (branch migration). Although the RuvAB complex served as a paradigm for the processing of the Holliday junction, due to technical limitations the detailed structure and underlying mechanism of the RuvAB branch migration complex has until now remained unclear. Recently, structures of a reconstituted RuvAB complex actively-processing a Holliday junction were resolved using time-resolved cryo-electron microscopy. These structures showed distinct conformational states at different stages of the migration process. These structures made it possible to propose an integrated model for RuvAB Holliday junction branch migration. Furthermore, they revealed unexpected insights into the highly coordinated and regulated mechanisms of the nucleotide cycle powering substrate translocation in the hexameric AAA+ RuvB ATPase. Here, we review these latest advances and describe areas for future research.

Single-molecule insight into stalled replication fork rescue in Escherichia coli

DNA replication forks stall at least once per cell cycle in Escherichia coli. DNA replication must be restarted if the cell is to survive. Restart is a multi-step process requiring the sequential action of several proteins whose actions are dictated by the nature of the impediment to fork progression. When fork progress is impeded, the sequential actions of SSB, RecG and the RuvABC complex are required for rescue. In contrast, when a template discontinuity results in the forked DNA breaking apart, the actions of the RecBCD pathway enzymes are required to resurrect the fork so that replication can resume. In this review, we focus primarily on the significant insight gained from single-molecule studies of individual proteins, protein complexes, and also, partially reconstituted regression and RecBCD pathways. This insight is related to the bulk-phase biochemical data to provide a comprehensive review of each protein or protein complex as it relates to stalled DNA replication fork rescue.

Viral and cellular SOS-regulated motor proteins: dsDNA translocation mechanisms with divergent functions

DNA damage attacks on bacterial cells have been known to activate the SOS response, a transcriptional response affecting chromosome replication, DNA recombination and repair, cell division and prophage induction. All these functions require double-stranded (ds) DNA translocation by ASCE hexameric motors. This review seeks to delineate the structural and functional characteristics of the SOS response and the SOS-regulated DNA translocases FtsK and RuvB with the phi29 bacteriophage packaging motor gp16 ATPase as a prototype to study bacterial motors. While gp16 ATPase, cellular FtsK and RuvB are similarly comprised of hexameric rings encircling dsDNA and functioning as ATP-driven DNA translocases, they utilize different mechanisms to accomplish separate functions, suggesting a convergent evolution of these motors. The gp16 ATPase and FtsK use a novel revolution mechanism, generating a power stroke between subunits through an entropy-DNA affinity switch and pushing dsDNA inward without rotation of DNA and the motor, whereas RuvB seems to employ a rotation mechanism that remains to be further characterized. While FtsK and RuvB perform essential tasks during the SOS response, their roles may be far more significant as SOS response is involved in antibiotic-inducible bacterial vesiculation and biofilm formation as well as the perspective of the bacteria-cancer evolutionary interaction.

Characterization of the ATPase activity of RecG and RuvAB proteins on model fork structures reveals insight into stalled DNA replication fork repair

RecG and RuvAB are proposed to act at stalled DNA replication forks to facilitate replication restart. To clarify the roles of these proteins in fork regression, we used a coupled spectrophotometric ATPase assay to determine how these helicases act on two groups of model fork substrates: the first group mimics nascent stalled forks, whereas the second mimics regressed fork structures. The results show that RecG is active on the substrates in group 1, whereas these are poor substrates for RuvAB. In addition, in the presence of group 1 forks, the single-stranded DNA-binding protein (SSB) enhances the activity of RecG and enables it to compete with excess RuvA. In contrast, SSB inhibits the activity of RuvAB on these substrates. Results also show that the preferred regressed fork substrate for RuvAB is a Holliday junction, not a forked DNA. The active form of the enzyme on the Holliday junction contains a single RuvA tetramer. In contrast, although the enzyme is active on a regressed fork structure, RuvB loading by a single RuvA tetramer is impaired, and full activity requires the cooperative binding of two forked DNA substrate molecules. Collectively, the data support a model where RecG is responsible for stalled DNA replication fork regression. SSB ensures that if the nascent fork has single-stranded DNA character RuvAB is inhibited, whereas the activity of RecG is preferentially enhanced. Only once the fork has been regressed and the DNA is relaxed can RuvAB bind to a RecG-extruded Holliday junction.

DNA Helicases

DNA and RNA helicases are organized into six superfamilies of enzymes on the basis of sequence alignments, biochemical data, and available crystal structures. DNA helicases, members of which are found in each of the superfamilies, are an essential group of motor proteins that unwind DNA duplexes into their component single strands in a process that is coupled to the hydrolysis of nucleoside 5'-triphosphates. The purpose of this DNA unwinding is to provide nascent, single-stranded DNA (ssDNA) for the processes of DNA repair, replication, and recombination. Not surprisingly, DNA helicases share common biochemical properties that include the binding of single- and double-stranded DNA, nucleoside 5'-triphosphate binding and hydrolysis, and nucleoside 5'-triphosphate hydrolysis-coupled, polar unwinding of duplex DNA. These enzymes participate in every aspect of DNA metabolism due to the requirement for transient separation of small regions of the duplex genome into its component strands so that replication, recombination, and repair can occur. In Escherichia coli, there are currently twelve DNA helicases that perform a variety of tasks ranging from simple strand separation at the replication fork to more sophisticated processes in DNA repair and genetic recombination. In this chapter, the superfamily classification, role(s) in DNA metabolism, effects of mutations, biochemical analysis, oligomeric nature, and interacting partner proteins of each of the twelve DNA helicases are discussed.

Three-dimensional structural views of branch migration and resolution in DNA homologous recombination

The processing of the Holliday junction by various proteins is a major event in DNA homologous recombination and is crucial to the maintenance of genome stability and biological diversity. The proteins RuvA, RuvB and RuvC play central roles in the late stage of recombination in prokaryotes. Recent atomic views of these proteins, including protein-protein and protein-junction DNA complexes, provide new insights into branch migration mechanisms: RuvA is likely to be responsible for base-pair rearrangements, whereas RuvB, classified as a member of the AAA(+) family, functions as a pump to pull DNA duplex arms without segmental unwinding. The mechanism of junction resolution by RuvC in the RuvABC resolvasome remains to be elucidated.

Crystal structure of the RuvA-RuvB complex: a structural basis for the Holliday junction migrating motor machinery

We present the X-ray structure of the RuvA-RuvB complex, which plays a crucial role in ATP-dependent branch migration. Two RuvA tetramers form the symmetric and closed octameric shell, where four RuvA domain IIIs spring out in the two opposite directions to be individually caught by a single RuvB. The binding of domain III deforms the protruding beta hairpin in the N-terminal domain of RuvB and thereby appears to induce a functional and less symmetric RuvB hexameric ring. The model of the RuvA-RuvB junction DNA ternary complex, constructed by fitting the X-ray structure into the averaged electron microscopic images of the RuvA-RuvB junction, appears to be more compatible with the branch migration mode of a fixed RuvA-RuvB interaction than with a rotational interaction mode.

Mutational analysis of the functional motifs of RuvB, an AAA+ class helicase and motor protein for holliday junction branch migration

Escherichia coli RuvB protein, together with RuvA, promotes branch migration of Holliday junctions during homologous recombination and recombination repair. The RuvB molecular motor is an intrinsic ATP-dependent DNA helicase with a hexameric ring structure and its architecture has been suggested to be related to those of the members of the AAA+ protein class. In this study, we isolated a large number of plasmids carrying ruvB mutant genes and identified amino acid residues important for the RuvB functions by examining the in vivo DNA repair activities of the mutant proteins. Based on these mutational studies and amino acid conservation among various RuvBs, we identified 10 RuvB motifs that agreed well with the features of the AAA+ protein class and that distinguished the primary structure of RuvB from that of typical DNA/RNA helicases with seven conserved helicase motifs.

Processing of recombination intermediates by the RuvABC proteins

The RuvA, RuvB, and RuvC proteins in Escherichia coli play important roles in the late stages of homologous genetic recombination and the recombinational repair of damaged DNA. Two proteins, RuvA and RuvB, form a complex that promotes ATP-dependent branch migration of Holliday junctions, a process that is important for the formation of heteroduplex DNA. Individual roles for each protein have been defined, with RuvA acting as a specificity factor that targets RuvB, the branch migration motor to the junction. Structural studies indicate that two RuvA tetramers sandwich the junction and hold it in an unfolded square-planar configuration. Hexameric rings of RuvB face each other across the junction and promote a novel dual helicase action that "pumps" DNA through the RuvAB complex, using the free energy provided by ATP hydrolysis. The third protein, RuvC endonuclease, resolves the Holliday junction by introducing nicks into two DNA strands. Genetic and biochemical studies indicate that branch migration and resolution are coupled by direct interactions between the three proteins, possibly by the formation of a RuvABC complex.

Role of RuvA in branch migration reactions catalyzed by the RuvA and RuvB proteins of Escherichia coli

The RuvA and RuvB proteins of Escherichia coli promote ATP-dependent branch migration of Holliday junctions during homologous genetic recombination and DNA repair. In this process, RuvA acts as a specificity factor that targets RuvB, a hexameric ring motor protein, to the junction. Because elevated concentrations of RuvB can promote branch migration in the absence of RuvA, it has been suggested that RuvA acts as a molecular matchmaker. In the studies presented here, we compared the requirements for RuvAB- and RuvB-mediated branch migration reactions and found that reactions catalyzed by RuvB alone were highly sensitive to inhibition by NaCl, temperature, ADP, and ATPgammaS. Our observations indicate that the two reactions occur by distinct mechanisms and support the notion that RuvAB-mediated branch migration is physiologically more relevant than that catalyzed by RuvB. We also show that ongoing RuvAB-mediated branch migration reactions were blocked by the addition of polyclonal antibodies raised against RuvA. The role of RuvA is therefore unlikely to be restricted to RuvB targeting; instead, it is required continually during branch migration. Competition with excess synthetic Holliday junctions, sufficient to sequester released RuvA, failed to cause an immediate block and leads us to suggest that RuvAB promote branch migration by a processive mechanism.