RuvC protein resolves Holliday junctions via cleavage of the continuous (noncrossover) strands

Interactions between RuvA and RuvC at Holliday junctions: inhibition of junction cleavage and formation of a RuvA-RuvC-DNA complex

The RuvAB and RuvC enzymes of Escherichia coli define a molecular pathway for the resolution of Holliday intermediates in recombination and DNA repair. They bind specifically to Holliday junctions, and catalyse their branch migration and cleavage, respectively. In a RuvA(B)-junction complex, the Holliday structure is held in an open (square planar) configuration on the concave surface of a 4-fold symmetrical tetramer of RuvA, whereas in a RuvC-junction complex it is folded in an alternative arrangement as part of the cleavage reaction. Genetic studies have shown that the activity of RuvC in vivo depends on RuvAB, which suggests that the two enzymes act in concert, with junction cleavage by RuvC following from branch migration by RuvAB. We have investigated how RuvC can take over a junction from RuvAB to cleave the DNA. We show that RuvA inhibits junction cleavage by RuvC, probably by sandwiching the junction between two tetramers. The extent of inhibition depends on the reaction kinetics of RuvA binding relative to RuvC binding and cleavage. The presence of RuvB and the concentration of Mg2+ both have a significant effect on cleavage in the presence of RuvA. However, a novel protein-DNA complex can be formed when junction DNA is incubated with both RuvA and RuvC. Its mobility is consistent with a RuvC dimer binding to a junction held in an open configuration on the surface of a RuvA tetramer. We suggest that this arrangement provides RuvC with the means to scan the junction during the RuvAB-mediated branch migration reaction for DNA sequences that it can cleave. We further suggest that recognition of the target may provide a trigger for dissociating RuvA, allowing the junction to be folded and cleaved by RuvC.

Resolution of Holliday junctions in genetic recombination: RuvC protein nicks DNA at the point of strand exchange

The RuvC protein of Escherichia coli catalyzes the resolution of recombination intermediates during genetic recombination and the recombinational repair of damaged DNA. Resolution involves specific recognition of the Holliday structure to form a complex that exhibits twofold symmetry with the DNA in an open configuration. Cleavage occurs when strands of like polarity are nicked at the sequence 5'-WTT decreases S-3' (where W is A or T and S is G or C). To determine whether the cleavage site needs to be located at, or close to, the point at which DNA strands exchange partners, Holliday structures were constructed with the junction points at defined sites within this sequence. We found that the efficiency of resolution was optimal when the cleavage site was coincident with the position of DNA strand exchange. In these studies, junction targeting was achieved by incorporating uncharged methyl phosphonates into the DNA backbone, providing further evidence for the importance of charge-charge repulsions in determining DNA structure.

Analysis of substrate specificity of the RuvC holliday junction resolvase with synthetic Holliday junctions

The Escherichia coli RuvC protein endonucleolytically resolves Holliday junctions, which are formed as intermediates during genetic recombination and recombination repair. Previous studies using model Holliday junctions suggested that a certain size of central core of homology and a specific sequence in the junction were required for efficient cleavage by RuvC, although not for binding. To determine the minimum length of sequence homology required for RuvC cleavage, we made a series of synthetic Holliday junctions with various lengths of homologous sequence in the core region. It was demonstrated that a monomobile junction possessing only 2 base pairs of the homology core was efficiently cleaved by RuvC. To study the sequence specificity for cleavage, we made 16 bimobile junctions, which differed only in the homologous core sequence. Among them, 6 junctions were efficiently cleaved. Cleavage occurred by introduction of nicks symmetrically at the 3'-side of thymine in all cases. However, the nucleotide bases at the 3'-side of the thymines were not always identical between the two strands nicked. These results suggest that RuvC recognizes mainly topological symmetry of the Holliday junction but not the sequence symmetry per se, that the thymine residue at the cleavage site plays an important role for RuvC-mediated resolution, and that a long homologous core sequence is not essential for cleavage.

Crystal structure of DNA recombination protein RuvA and a model for its binding to the Holliday junction

The Escherichia coli DNA binding protein RuvA acts in concert with the helicase RuvB to drive branch migration of Holliday intermediates during recombination and DNA repair. The atomic structure of RuvA was determined at a resolution of 1.9 angstroms. Four monomers of RuvA are related by fourfold symmetry in a manner reminiscent of a four-petaled flower. The four DNA duplex arms of a Holliday junction can be modeled in a square planar configuration and docked into grooves on the concave surface of the protein around a central pin that may facilitate strand separation during the migration reaction. The model presented reveals how a RuvAB-junction complex may also accommodate the resolvase RuvC.

Unraveling the late stages of recombinational repair: metabolism of DNA junctions in Escherichia coli

DNA junctions are by-products of recombinational repair, during which a damaged DNA sequence, assisted by RecA filament, invades an intact homologous DNA to form a joint molecule. The junctions are three-strand or four-strand depending on how many single DNA strands participate in joint molecules. In E. coli, at least two independent pathways to remove the junctions are proposed to operate. One is via RuvAB-promoted migration of four-strand junctions with their subsequent resolution by RuvC. In vivo, RuvAB and RuvC enzymes might work in a single complex, a resolvasome, to clean DNA from used RecA filaments and to resolve four-strand junctions. An alternative pathway for junction removal could be via RecG-promoted branch migration of three-strand junctions, provided that an as yet uncharacterized endonuclease activity incises one of the strands in the joint molecules.

Roles of electrostatic interaction in proteins

More than 60 years after the analyses by Linderstrom-Lang and Kirkwood of their hypothetical 'protein' structures, we have now a plethora of experimental evidence and computational estimates of the electrostatic forces in proteins, with very many protein 3D structures at atomic resolution. In the mean time, there were in the beginning, many arguments and suggestions about the roles of electrostatics, mainly from empirical findings and tendencies. A few experimental results indicated that the electrostatic contribution is of the order of several kcal/mol, which was theoretically difficult to reproduce correctly, because a large opposing reaction field should be subtracted from a large, direct Coulombic field. Although the importance of the reaction field was recognized even 70 years ago, appropriate applications to protein molecules were made only in this decade, with the development of numerical computation. Now, an electrostatic molecular surface is one of the most popular pictures in journals of structural biology, indicating that the electrostatic force is one of the important components contributing to molecular recognition, which is a major focus of current biology and biochemistry. The development of NMR techniques has made it possible to observe the individual ionizations of ionizable groups in a protein, in addition to the determination of the 3D structure. Since it does not require any additional probe, each charge state can report the very local and heterogeneous electrostatic potentials working in the protein, without disturbing the original field. From the pKa values, the contributions of electrostatic interactions, ion pairs, charge-dipole interactions, and hydrogen bonds to protein stability have been correctly evaluated. Protein engineering also provides much more information than that obtainable from the native proteins, as the residues concerned can now be easily substituted with other amino acid residues having electrostatically different characteristics. Those experimental results have revealed smaller contributions than previously expected, probably because we underestimated the reaction field effects. Especially, a single ion pair stabilizes a protein only slightly, although a cooperative salt-bridge network can contribute significantly to protein stability. Marginal stabilities of proteins arise from small difference between many factors with driving and opposing forces. In spite of the small contribution of each single electrostatic interaction to the protein stability, the sum of their actions works to maintain the specific 3D structure of the protein. The 'negative' roles of electrostatics, which might destabilize protein conformation, should be pointed out. Unpaired buried charges are energetically too expensive to exit in the hydrophobic core. Isolated hydrogen bond donors and acceptors also exert negative effects, but they are not as expensive as the unpaired buried charges, with costs of a few kcal/mol. Therefore, statistical analyses of protein 3D structures reveal only rare instances of isolated hydrogen bond donors and acceptors. This must be the main reason why alpha-helices and beta-sheets are only observed in protein cores as the backbone structures. Such secondary structures do not leave any backbone hydrogen donors or acceptors unpaired, because of their intrinsically regular packing. Otherwise, it might be very difficult to construct a backbone structure, in which all the backbone amide and carbonyl groups had their own hydrogen bond partners in the protein core. There are two theoretical approaches to protein electrostatics, the macroscopic or continuum model, and the microscopic or molecular model. As described in this article, the macroscopic model has inherent problems because the protein-solvent system is very hetergeneous from the physical point of view...

Characterisation of RuvAB-Holliday junction complexes by glycerol gradient sedimentation

The Escherichia coli RuvA and RuvB proteins interact specifically with Holliday junctions to promote ATP-dependent branch migration during genetic recombination and DNA repair. In the work described here, glycerol gradient centrifugation was used to investigate the requirements for the formation of pre-branch migration complexes. Since gradient centrifugation provides a simple and gentle method to analyse relatively unstable protein-DNA complexes, we were able to detect RuvA- and RuvAB-Holliday junction complexes without the need for chemical fixation. Using 35S-labelled RuvA protein and 3H-labelled Holliday junctions, we show that RuvA acts as a helicase accessory factor that loads the RuvB helicase onto the Holliday junction by structure-specific interactions. The resulting complex contained both RuvA and RuvB, as detected by Western blotting using serum raised against RuvA and RuvB. The stoichiometry of binding was estimated to be approximately four RuvA tetramers per junction. Formation of the RuvAB-Holliday junction complex required the presence of divalent metal ions and occurred without the need for ATP. However, the stability of the complex was enhanced by the presence of ATP gamma S, a non-hydrolysable ATP analogue. The data support a model for branch migration in which structure-specific binding of Holliday junctions by RuvA targets the assembly of hexameric RuvB rings on DNA. Specific loading of the RuvB ring helicase by RuvA is likely to be the initial step towards ATP-dependent branch migration.