Coordination and internal exchange of two DNA molecules in a RecA filament in the presence of hydrolysing ATP. Information on ATP-RecA-DNA structure from linear dichroism spectroscopy

DNA dynamics in RecA-DNA filaments: ATP hydrolysis-related flexibility in DNA

RecA-catalyzed DNA recombination is initiated by a mandatory, high-energy form of DNA in RecA-nucleoprotein filaments, where bases are highly unstacked and the backbone is highly unwound. Interestingly, only the energetics consequent to adenosine triphosphate (ATP) binding, rather than its hydrolysis, seems sufficient to mediate such a high-energy structural hallmark of a recombination filament. The structural consequence of ATP hydrolysis on the DNA part of the filament thus remains largely unknown. We report time-resolved fluorescence dynamics of bases in RecA-DNA complexes and demonstrate that DNA bases in the same exhibit novel, motional dynamics with a rotational correlation time of 7-10 ns, specifically in the presence of ATP hydrolysis. When the ongoing ATP hydrolysis of RecA-DNA filament is "poisoned" by a nonhydrolyzable form of ATP (ATPgammaS), the motional dynamics cease and reveal a global motion with a rotational correlation time of >20 ns. Such ATP hydrolysis-induced flexibility ensues in single-stranded as well as double-stranded bases of RecA-DNA filaments. These results suggest that the role of ATP hydrolysis is to induce a high level of backbone flexibility in RecA-DNA filament, a dynamic property that is likely to be important for efficient strand exchanges in ATP hydrolysis specific RecA reactions. It is the absence of these motions that may cause high rigidity in RecA-DNA filaments in ATPgammaS. Dynamic light scattering measurement comparisons of RecA-ss-DNA filaments formed in ATPgammaS vs that of ATP confirmed such an interpretation, where the former showed a complex of larger (30 nm) hydrodynamic radius than that of latter (12-15 nm). Taken together, these results reveal a more dynamic state of DNA in RecA-DNA filament that is hydrolyzing ATP, which encourage us to model the role of ATP hydrolysis in RecA-mediated DNA transactions.

Difference between active and inactive nucleotide cofactors in the effect on the DNA binding and the helical structure of RecA filament dissociation of RecA--DNA complex by inactive nucleotides

The RecA protein requires ATP or dATP for its coprotease and strand exchange activities. Other natural nucleotides, such as ADP, CTP, GTP, UTP and TTP, have little or no activation effect on RecA for these activities. We have investigated the activation mechanism, and the selectivity for ATP, by studying the effect of various nucleotides on the DNA binding and the helical structure of the RecA filament. The interaction with DNA was investigated via fluorescence measurements with a fluorescent DNA analog and fluorescein-labeled oligonucleotides, assisted by linear dichroism. Filament structure was investigated via small-angle neutron scattering. There is no simple correlation between filament elongation, DNA binding affinity of RecA, and DNA structure in the RecA complex. There may be multiple conformations of RecA. Both coprotease and strand exchange activities require formation of a rigid and well organized complex. The triphosphate nucleotides which do not activate RecA, destabilize the RecA-DNA complex, indicating that the chemical nature of the nucleotide nucleobase is very important for the stability of RecA-DNA complex. Higher stability of the RecA-DNA complex in the presence of adenosine 5'-O-3-thiotriphosphate or guanosine 5'-O-3-thiotriphosphate than ATP or GTP indicates that contact between the protein and the chemical group at the gamma position of the nucleotide also affects the stability of the RecA-DNA complex. This contact appears also important for the rigid organization of DNA because ADP strongly decreases the rigidity of the complex.

Nucleotide dependent structural and kinetic changes in Xenopus rad51.1-DNA complex stimulating the strand exchange reaction: destacking of DNA bases and restriction of their local motion

Rad51 is a eukaryotic homologue of RecA and it catalyzes the DNA strand exchange reaction in homologous recombination. This protein, like RecA, requires ATP as a cofactor for activity. We investigated the mechanism of activation of this protein by the nucleotide cofactor by studying the effect of various nucleotides, particularly ATP, ADP and the non-hydrolyzable analog of ATP, adenosine-5'-O-(3-thiotriphosphate) (ATPgammaS) on the DNA binding of a Xenopus Rad51 protein (XRad51.1). DNA binding was studied in solution by monitoring the fluorescence changes of etheno-modified fluorescent poly(dA) or fluorescein-labeled oligo(dT) and by filter binding assay. Active nucleotides (ATP, dATP) changed the DNA binding mode of XRad51.1. In the active complex, the DNA bases were destacked and their motion was highly restricted. Dissociation of XRad51.1 from DNA was accelerated by ATP and dATP, as was dissociation of RecA from DNA. In contrast to these similarities with RecA, the XRad51.1-DNA complex was dissociated by the non-hydrolyzable analog of ATP (ATPgammaS) and this dissociation was not significantly accelerated by ADP. The effect of ATP hydrolysis on the XRad51.1-DNA complex differs from that on the RecA-DNA complex. ATP hydrolysis may not be essential for the strand exchange reaction whereas the changes in the DNA structure by ATP are important.

Kinetic analysis of pairing and strand exchange catalyzed by RecA. Detection by fluorescence energy transfer

RecA is a 38-kDa protein from Escherichia coli that polymerizes on single-stranded DNA, forming a nucleoprotein filament that pairs with homologous duplex DNA and carries out strand exchange in vitro. In this study, we measured RecA-catalyzed pairing and strand exchange in solution by energy transfer between fluorescent dyes on the ends of deoxyribo-oligonucleotides. By varying the position of the dyes in separate assays, we were able to detect the pairing of single-stranded RecA filament with duplex DNA as an increase in energy transfer, and strand displacement as a decrease in energy transfer. With these assays, the kinetics of pairing and strand displacement were studied by stopped-flow spectrofluorometry. The data revealed a rapid, second order, reversible pairing step that was followed by a slower, reversible, first order strand exchange step. These data indicate that an initial unstable intermediate exists which can readily return to reactants, and that a further, rate-limiting step (or steps) is required to effect or complete strand exchange.

The cofactor ATP in DNA-RecA complexes is not intercalated between DNA bases

In an attempt to understand the role of ATP as a cofactor at the interaction of the RecA protein with DNA, we have studied the orientation geometries of the cofactor analogs adenosine 5'-O-(3-thiotriphosphate) (ATP gamma S) and guanosine 5'-O-(3-thiotriphosphate) (GTP gamma S) in RecA-DNA complexes using flow linear dichroism spectroscopy. Both cofactors promote the formation of RecA-DNA complexes of similar structure as judged from similar orientations of DNA bases. The DNA orientation was probed through the dichroism of the long-wavelength absorption of a DNA analog, poly(d epsilon A). In this way differences between the dichroic spectra of the ATP gamma S-RecA-DNA and GTP gamma S-RecA-DNA complexes, observed in the shorter-wavelength region, are related to orientation at variations of the cofactor chromophores. The results show that the guanine plane of GTP gamma S is oriented parallel with the principal axis of the complex in contrast to the more perpendicular orientation of the DNA bases. This observation directly excludes the possibility that the cofactor could be intercalated between the DNA bases. The orientation of the adenine base of ATP gamma S, which may be similar to that of guanine of GTP gamma S albeit not exactly the same, is also inconsistent with intercalation. The possibility that the cofactor bound to the protein could be intercalated in DNA had been speculated from the observation that some DNA intercalators can induce RecA binding to DNA in the absence of cofactor.(ABSTRACT TRUNCATED AT 250 WORDS)

Biochemistry of homologous recombination in Escherichia coli

Homologous recombination is a fundamental biological process. Biochemical understanding of this process is most advanced for Escherichia coli. At least 25 gene products are involved in promoting genetic exchange. At present, this includes the RecA, RecBCD (exonuclease V), RecE (exonuclease VIII), RecF, RecG, RecJ, RecN, RecOR, RecQ, RecT, RuvAB, RuvC, SbcCD, and SSB proteins, as well as DNA polymerase I, DNA gyrase, DNA topoisomerase I, DNA ligase, and DNA helicases. The activities displayed by these enzymes include homologous DNA pairing and strand exchange, helicase, branch migration, Holliday junction binding and cleavage, nuclease, ATPase, topoisomerase, DNA binding, ATP binding, polymerase, and ligase, and, collectively, they define biochemical events that are essential for efficient recombination. In addition to these needed proteins, a cis-acting recombination hot spot known as Chi (chi: 5'-GCTGGTGG-3') plays a crucial regulatory function. The biochemical steps that comprise homologous recombination can be formally divided into four parts: (i) processing of DNA molecules into suitable recombination substrates, (ii) homologous pairing of the DNA partners and the exchange of DNA strands, (iii) extension of the nascent DNA heteroduplex; and (iv) resolution of the resulting crossover structure. This review focuses on the biochemical mechanisms underlying these steps, with particular emphases on the activities of the proteins involved and on the integration of these activities into likely biochemical pathways for recombination.

Accessibility to modification of histidine residues of RecA protein upon DNA and cofactor binding

The potential role of histidine residues of RecA protein in binding DNA has been investigated by monitoring their accessibility to diethylpyrocarbonate. In the absence of both DNA and cofactor, only one of two histidine residues is modified by the reagent, indicating that the other residue is buried. However, both histidine residues become accessible after addition of cofactor analog adenosine 5'-O-(3-thiotriphosphate) (ATP[S]) indicating a change in the organization of the RecA filament and/or a change in the conformation of protein. The diethylpyrocarbonate-modified RecA is found to be able to polymerize just as the unmodified protein. The binding of double-stranded DNA, in the presence of ATP[S], reduces the reactivity of both histidine residues to diethylpyrocarbonate. The binding of single-stranded DNA (with ATP[S]) has a similar, though smaller, protective effect. However, no significant dissociation of either of the complexes as a result of the modification was observed and a RecA molecule which had been modified in the absence of DNA could still bind DNA. A protection of the histidine residues is also effected by high salt concentration which promotes, just as DNA binding, ATPase and coprotease activity in RecA. The protection of histidine residues to diethylpyrocarbonate upon DNA binding probably relates to a conformational change of RecA and may not be any direct effect of shielding by the DNA. Nonetheless, the domains including the histidine residues could be centers of allosteric effects and are concluded to be close to the DNA binding site.