Inactivation of the recA protein by mutation of histidine 97 or lysine 248 at the subunit interface

Separation of recombination and SOS response in Escherichia coli RecA suggests LexA interaction sites

RecA plays a key role in homologous recombination, the induction of the DNA damage response through LexA cleavage and the activity of error-prone polymerase in Escherichia coli. RecA interacts with multiple partners to achieve this pleiotropic role, but the structural location and sequence determinants involved in these multiple interactions remain mostly unknown. Here, in a first application to prokaryotes, Evolutionary Trace (ET) analysis identifies clusters of evolutionarily important surface amino acids involved in RecA functions. Some of these clusters match the known ATP binding, DNA binding, and RecA-RecA homo-dimerization sites, but others are novel. Mutation analysis at these sites disrupted either recombination or LexA cleavage. This highlights distinct functional sites specific for recombination and DNA damage response induction. Finally, our analysis reveals a composite site for LexA binding and cleavage, which is formed only on the active RecA filament. These new sites can provide new drug targets to modulate one or more RecA functions, with the potential to address the problem of evolution of antibiotic resistance at its root.

In eubacteria, genome integrity is in large part orchestrated by RecA, which directly participates in recombination, induction of DNA damage response through LexA repressor cleavage and error-prone DNA synthesis. Yet, most of the interaction sites necessary for these vital processes are largely unknown. By comparing divergences among RecA sequences and computing putative functional regions, we discovered four functional sites of RecA. Targeted point-mutations were then tested for both recombination and DNA damage induction and reveal distinct RecA functions at each one of these sites. In particular, one new set of mutants is deficient in promoting LexA cleavage and yet maintains the ability to induce the DNA damage response. These results reveal specific amino acid determinants of the RecA–LexA interaction and suggest that LexA binds RecA_i and RecA_i+6 at a composite site on the RecA filament, which could explain the role of the active filament during LexA cleavage.

Molecular Design and Functional Organization of the RecA Protein

The bacterial RecA protein participates in a remarkably diverse set of functions, all of which are involved in the maintenance of genomic integrity. RecA is a central component in both the catalysis of recombinational DNA repair and the regulation of the cellular SOS response. Despite the mechanistic differences of its functions, all require formation of an active RecA/ATP/DNA complex. RecA is a classic allosterically regulated enzyme, and ATP binding results in a dramatic increase in DNA binding affinity and a cooperative assembly of RecA subunits to form an ordered, helical nucleoprotein filament. The molecular events that underlie this ATP-induced structural transition are becoming increasingly clear. This review focuses on descriptions of our current understanding of the molecular design and allosteric regulation of RecA. We present a comprehensive list of all published recA mutants and use the results of various genetic and biochemical studies, together with available structural information, to develop ideas regarding the design of RecA functional domains and their catalytic organization.

Defective dissociation of a "slow" RecA mutant protein imparts an Escherichia coli growth defect

The RecA and some related proteins possess a simple motif, called (KR)X(KR), that (in RecA) consists of two lysine residues at positions 248 and 250 at the subunit-subunit interface. This study and previous work implicate this RecA motif in the following: (a) catalyzing ATP hydrolysis in trans,(b) coordinating the ATP hydrolytic cycles of adjacent subunits, (c) governing the rate of ATP hydrolysis, and (d) coupling the ATP hydrolysis to work (in this case DNA strand exchange). The conservative K250R mutation leaves RecA nucleoprotein filament formation largely intact. However, ATP hydrolysis is slowed to less than 15% of the wild-type rate. DNA strand exchange is also slowed commensurate with the rate of ATP hydrolysis. The results reinforce the idea of a tight coupling between ATP hydrolysis and DNA strand exchange. When a plasmid-borne RecA K250R protein is expressed in a cell otherwise lacking RecA protein, the growth of the cells is severely curtailed. The slow growth defect is alleviated in cells lacking RecFOR function, suggesting that the defect reflects loading of RecA at stalled replication forks. Suppressors occur as recA gene alterations, and their properties indicate that limited dissociation by RecA K250R confers the slow growth phenotype. Overall, the results suggest that recombinational DNA repair is a common occurrence in cells. RecA protein plays a sufficiently intimate role in the bacterial cell cycle that its properties can limit the growth rate of a bacterial culture.

Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures

The RecA family of ATPases mediates homologous recombination, a reaction essential for maintaining genomic integrity and for generating genetic diversity. RecA, ATP and single-stranded DNA (ssDNA) form a helical filament that binds to double-stranded DNA (dsDNA), searches for homology, and then catalyses the exchange of the complementary strand, producing a new heteroduplex. Here we have solved the crystal structures of the Escherichia coli RecA-ssDNA and RecA-heteroduplex filaments. They show that ssDNA and ATP bind to RecA-RecA interfaces cooperatively, explaining the ATP dependency of DNA binding. The ATP gamma-phosphate is sensed across the RecA-RecA interface by two lysine residues that also stimulate ATP hydrolysis, providing a mechanism for DNA release. The DNA is underwound and stretched globally, but locally it adopts a B-DNA-like conformation that restricts the homology search to Watson-Crick-type base pairing. The complementary strand interacts primarily through base pairing, making heteroduplex formation strictly dependent on complementarity. The underwound, stretched filament conformation probably evolved to destabilize the donor duplex, freeing the complementary strand for homology sampling.

Complementation of one RecA protein point mutation by another. Evidence for trans catalysis of ATP hydrolysis

The RecA residues Lys248 and Glu96 are closely opposed across the RecA subunit-subunit interface in some recent models of the RecA nucleoprotein filament. The K248R and E96D single mutant proteins of the Escherichia coli RecA protein each bind to DNA and form nucleoprotein filaments but do not hydrolyze ATP or dATP. A mixture of K248R and E96D single mutant proteins restores dATP hydrolysis to 25% of the wild type rate, with maximum restoration seen when the proteins are present in a 1:1 ratio. The K248R/E96D double mutant RecA protein also hydrolyzes ATP and dATP at rates up to 10-fold higher than either single mutant, although at a reduced rate compared with the wild type protein. Thus, the K248R mutation partially complements the inactive E96D mutation and vice versa. The complementation is not sufficient to allow DNA strand exchange. The K248R and E96D mutations originate from opposite sides of the subunit-subunit interface. The functional complementation suggests that Lys248 plays a significant role in ATP hydrolysis in trans across the subunit-subunit interface in the RecA nucleoprotein filament. This could be part of a mechanism for the long range coordination of hydrolytic cycles between subunits within the RecA filament.

Crystal structures of Escherichia coli RecA in a compressed helical filament

The X-ray crystal structure of uncomplexed Escherichia coli RecA protein has been determined in three new crystal forms at resolutions of 1.9 A, 2.0 A, and 2.6 A. The RecA protein used for this study contains the extra residues Gly-Ser-His-Met at the N terminus, but retains normal ssDNA-dependent ATPase and coprotease activities. In all three crystals, RecA is packed in a right-handed helical filament with a pitch of approximately 74 A. These RecA filaments are compressed relative to the original crystal structure of RecA, which has a helical pitch of 82.7 A. In the structures of the compressed RecA filament, the monomer-monomer interface and the core domain are essentially the same as in the RecA structure with the 83 A pitch. The change in helical pitch is accommodated by a small movement of the N-terminal domain, which is reoriented to preserve the contacts it makes at the monomer-monomer interface. The new crystal structures show significant variation in the orientation and conformation of the C-terminal domain, as well as in the inter-filament packing interactions. In crystal form 2, a calcium ion is bound closely to a beta-hairpin of the C-terminal domain and to Asp38 of a neighboring filament, and residues 329-331 of the C-terminal tail become ordered to contact a neighboring filament. In crystal forms 3 and 4, a sulfate ion or a phosphate anion is bound to the same site on RecA as the beta-phosphate group of ADP, causing an opening of the P-loop. Altogether, the structures show the conformational variability of RecA protein in the crystalline state, providing insight into many aspects of RecA function.

ATP-mediated conformational changes in the RecA filament

The crystal structure of the E. coli RecA protein was solved more than 10 years ago, but it has provided limited insight into the mechanism of homologous genetic recombination. Using electron microscopy, we have reconstructed five different states of RecA-DNA filaments. The C-terminal lobe of the RecA protein is modulated by the state of the distantly bound nucleotide, and this allosteric coupling can explain how mutations and truncations of this C-terminal lobe enhance RecA's activity. A model generated from these reconstructions shows that the nucleotide binding core is substantially rotated from its position in the RecA crystal filament, resulting in ATP binding between subunits. This simple rotation can explain the large cooperativity in ATP hydrolysis observed for RecA-DNA filaments.

The bacterial RecA protein and the recombinational DNA repair of stalled replication forks

The primary function of bacterial recombination systems is the nonmutagenic repair of stalled or collapsed replication forks. The RecA protein plays a central role in these repair pathways, and its biochemistry must be considered in this context. RecA protein promotes DNA strand exchange, a reaction that contributes to fork regression and DNA end invasion steps. RecA protein activities, especially formation and disassembly of its filaments, affect many additional steps. So far, Escherichia coli RecA appears to be unique among its nearly ubiquitous family of homologous proteins in that it possesses a motorlike activity that can couple the branch movement in DNA strand exchange to ATP hydrolysis. RecA is also a multifunctional protein, serving in different biochemical roles for recombinational processes, SOS induction, and mutagenic lesion bypass. New biochemical and structural information highlights both the similarities and distinctions between RecA and its homologs. Increasingly, those differences can be rationalized in terms of biological function.

Biochemical characterization of the human RAD51 protein. III. Modulation of DNA binding by adenosine nucleotides

Adenosine nucleotides affect the ability of RecA small middle dotsingle-stranded DNA (ssDNA) nucleoprotein filaments to cooperatively assume and maintain an extended structure that facilitates DNA pairing during recombination. Here we have determined that ADP and ATP/ATPgammaS affect the DNA binding and aggregation properties of the human RecA homolog human RAD51 protein (hRAD51). These studies have revealed significant differences between hRAD51 and RecA. In the presence of ATPgammaS, RecA forms a stable complex with ssDNA, while the hRAD51 ssDNA complex is destabilized. Conversely, in the presence of ADP and ATP, the RecA ssDNA complex is unstable, while the hRAD51 ssDNA complex is stabilized. We identified two hRAD51 small middle dotssDNA binding forms by gel shift analysis, which were distinct from a well defined RecA small middle dotssDNA binding form. The available evidence suggests that a low molecular weight hRAD51 small middle dotssDNA binding form (hRAD51 small middle dotssDNA(low)) correlates with active ADP and ATP processing. A high molecular weight hRAD51 small middle dotssDNA aggregate (hRAD51 small middle dotssDNA(high)) appears to correlate with a form that fails to process ADP and ATP. Our data are consistent with the notion that hRAD51 is unable to appropriately coordinate ssDNA binding with adenosine nucleotide processing. These observations suggest that other factors may assist hRAD51 in order to mirror RecA recombinational function.

[L29M] substitution in the interface of subunit-subunit interactions enhances Escherichia coli RecA protein properties important for its recombinogenic activity

Genetic analysis of RecA protein chimeras and their ancestors, RecAEc (from Escherichia coli) and RecAPa (Pseudomonas aeruginosa) had allowed us to place these proteins with respect to their recombinogenic activities in the following order: RecAPa>RecAX21>RecAX20=RecAEc. While RecAX20 differs from RecAEc in five amino acid residues with two substitutions ([S25A] and [I26V]) at the interface of subunit interactions in the RecA polymer, RecAX20 and RecAX21 differ only by a single substitution [L29M] present at the interface. Here, we present an analysis of the biochemical properties considered important for the recombinogenic activity of all four RecA proteins. While RecAX20 was very similar to RecAEc by all activities analysed, RecAX21 differed from RecAEc in several respects. These differences included an increased affinity for double-stranded DNA, a more active displacement of SSB protein from single-stranded DNA (ssDNA), a decreased end-dependent RecAX21 protein dissociation from a presynaptic complex, and a greater accumulation of intermediate products relative to the final product in the strand-exchange reaction. RecAPa was more tolerant than RecAX21 only to the end-dependent RecA protein dissociation. In addition, RecAPa was more resistant to temperature and salt concentrations in its ability to form a presynaptic RecAPa::ATP::ssDNA filament. Calculations of conformational energy revealed that the [L29M] substitution in RecAX21 polymer caused an increase in its flexibility. This led us to conclude that even a small change in the flexibility of the RecA presynaptic complex could profoundly affect its recombinogenic properties.

Mutations in the N-terminal region of RecA that disrupt the stability of free protein oligomers but not RecA-DNA complexes

We have introduced targeted mutations in two areas that make up part of the RecA subunit interface. In the RecA crystal structure, cross-subunit interactions are observed between the Lys6 and Asp139 side-chains, and between the Arg28 and Asn113 side-chains. Unexpectedly, we find that mutations at Lys6 and Arg28 impose sever defects on the oligomeric stability of free RecA protein, whereas mutations at Asn113 or Asp139 do not. However, Lys6 and Arg28 mutant proteins showed an apparent normal formation of RecA-DNA complexes. These results suggest that cross-subunit contacts in this region of the protein are different for free RecA protein filaments versus RecA-DNA nucleoprotein filaments. Mutant proteins with substitutions at either Lys6 or Arg28 show partial inhibition of DNA strand exchange activity, yet the mechanistic reasons for this inhibition appear to be distinct. Although Lys6 and Arg28 appear to be more important to the stability of free RecA protein, as opposed to the stability of the catalytically active nucleoprotein filament, our results support the idea that the cross-subunit interactions made by each residue play an important role in optimizing the catalytic organization of the active RecA oligomer.

Analysis of Escherichia coli RecA interactions with LexA, lambda CI, and UmuD by site-directed mutagenesis of recA

An early event in the induction of the SOS system of Escherichia coli is RecA-mediated cleavage of the LexA repressor. RecA acts indirectly as a coprotease to stimulate repressor self-cleavage, presumably by forming a complex with LexA. How complex formation leads to cleavage is not known. As an approach to this question, it would be desirable to identify the protein-protein interaction sites on each protein. It was previously proposed that LexA and other cleavable substrates, such as phage lambda CI repressor and E. coli UmuD, bind to a cleft located between two RecA monomers in the crystal structure. To test this model, and to map the interface between RecA and its substrates, we carried out alanine-scanning mutagenesis of RecA. Twenty double mutations were made, and cells carrying them were characterized for RecA-dependent repair functions and for coprotease activity towards LexA, lambda CI, and UmuD. One mutation in the cleft region had partial defects in cleavage of CI and (as expected from previous data) of UmuD. Two mutations in the cleft region conferred constitutive cleavage towards CI but not towards LexA or UmuD. By contrast, no mutations in the cleft region or elsewhere in RecA were found to specifically impair the cleavage of LexA. Our data are consistent with binding of CI and UmuD to the cleft between two RecA monomers but do not provide support for the model in which LexA binds in this cleft.

Enhanced monomer-monomer interactions can suppress the recombination deficiency of the recA142 allele

The RecA142 protein, in which valine is substituted for isoleucine-225, is defective for genetic recombination in vivo and for DNA strand exchange activity in vitro under conventional growth and reaction conditions respectively. However, we show that mildly acidic conditions restore both the in vitro DNA strand exchange activity and the in vivo function of RecA142 protein, suggesting that recombination function can be restored by a slight change in protein structure elicited by protonation. Indeed, we identified an intragenic suppressor of the recombination deficiency of the recA142 allele. This suppressor mutation is a substitution of leucine for glutamine at position 124. Based on the three-dimensional structure, the Q-124L substitution is predicted to make a new monomer-monomer contact with residue phenylalanine-21 of the adjacent RecA monomer. The Q-124L mutation is not allele specific, because it also suppresses the recombination deficiency of a recA deletion (Delta9), lacking nine amino acids at the amino-terminus, presumably by reinforcing the monomer-monomer interactions that are attenuated by the Delta9 deletion. Expression of RecA(Q-124L) protein is toxic to Escherichia coli, presumably because of enhanced affinity for DNA. We speculate as to how enhanced monomer-monomer interactions and acidic pH conditions can restore the recombination activity of some defective recA alleles.

Quantitative analysis of the kinetics of end-dependent disassembly of RecA filaments from ssDNA

On linear single-stranded DNA, RecA filaments assemble and disassemble in the 5' to 3' direction. Monomers (or other units) associate at one end and dissociate from the other. ATP hydrolysis occurs throughout the filament. Dissociation can result when ATP is hydrolyzed by the monomer at the disassembly end. We have developed a comprehensive model for the end-dependent filament disassembly process. The model accounts not only for disassembly, but also for the limited reassembly that occurs as DNA is vacated by disassembling filaments. The overall process can be monitored quantitatively by following the resulting decline in DNA-dependent ATP hydrolysis. The rate of disassembly is highly pH dependent, being negligible at pH 6 and reaching a maximum at pH values above 7. 5. The rate of disassembly is not significantly affected by the concentration of free RecA protein within the experimental uncertainty. For filaments on single-stranded DNA, the monomer kcat for ATP hydrolysis is 30 min-1, and disassembly proceeds at a maximum rate of 60-70 monomers per minute per filament end. The latter rate is that predicted if the ATP hydrolytic cycles of adjacent monomers are not coupled in any way.

Toxic mutations in the recA gene of E. coli prevent proper chromosome segregation

The recA gene of Escherichia coli is the prototype of the recA/RAD51/DMC1/uvsX gene family of strand transferases involved in genetic recombination. In order to find mutations in the recA gene important in catalytic turnover, a genetic screen was conducted for dominant lethal mutants. Eight single amino acid substitution mutants were found to prevent proper chromosome segregation and to kill cells in the presence or absence of an inducible SOS system. All mutants catalyzed some level of recombination and constitutively stimulated LexA cleavage. The mutations occur at the monomer-monomer interface of the RecA polymer or at residues important in ATP hydrolysis, implicating these residues in catalytic turnover. Based on an analysis of the E96D mutant, a model is presented in which slow RecA-DNA dissociation prevents chromosome segregation, engendering lexA-independent, lethal filamentation of cells.

Characterization of RecA1332 in vivo and in vitro. A role for alpha-helix E as a liaison between the subunit-subunit interface and the DNA and ATP binding domains of RecA protein

BACKGROUND

The RecA protein of Escherichia coli is essential for homologous recombination and induction of the SOS response. RecA has three cysteines located at positions 90, 116 and 129. Chemical modification of these residues abolishes ATP hydrolysis and repressor cleavage, and causes a reduction in the DNA strand exchange and DNA strand annealing activities. Several mutants at each of these positions were isolated and partially characterized. One of these, recA1332, replaces cysteine 129 with methionine. Although this is a relatively conservative mutation based on hydrophobicity, recA1332 was completely defective for DNA repair but the purified protein was active for ATPase in vitro.

RESULTS

In vivo, strains containing this mutant allele were shown to be defective when assayed for all RecA-dependent activities. In vitro, RecA1332 protein possessed DNA-dependent ATP hydrolysis activity that showed an increased sensitivity to inhibition by monovalent cations, and whose k(cat) was reduced 3- to 12-fold. In addition, RecA1332 was unable to use oligodeoxyribonulceotides as ssDNA cofactors in the ATPase reaction. RecA1332 showed altered binding to single- and double-stranded DNA and, although it was able to perform DNA strand exchange, it was slowed in its ability to both form joint molecule intermediates and to convert these species to product.

CONCLUSIONS

Our results are consistent with a defect in intermolecular interactions between RecA monomers. We propose that alpha-helix E (which includes C129M) is a liaison that connects the subunit-subunit interactions to DNA and ATP binding, thereby creating filament stability and cooperativity.

Mutant RecA proteins which form hexamer-sized oligomers

We have analyzed the oligomeric properties of a number of mutant RecA proteins containing single amino acid substitutions within one region of the subunit interface. In contrast to wild-type RecA, which forms a heterogeneous population of different-sized oligomers, we find that many of these mutant proteins exist in a more homogeneous oligomeric form, which approximates to the size of a RecA hexamer. Some of these mutants have a significant level of activity in vivo for recombinational DNA repair and thus represent the first mutant RecA proteins identified which retain activity yet can exist in a discrete oligomeric state as free protein.

Locations of functional domains in the RecA protein. Overlap of domains and regulation of activities

We review the locations of various functional domains of the RecA protein of Escherichia coli, including how they have been assigned, and discuss the potential regulatory roles of spatial overlap between different domains. RecA is a multifunctional and ubiquitous protein involved both in general genetic recombination and in DNA repair: it regulates the synthesis and activity of DNA repair enzymes (SOS induction) and catalyses homologous recombination and mutagenesis. For these activities RecA interacts with a nucleotide cofactor, single-stranded and double-stranded DNAs, the LexA repressor, UmuD protein, the UmuD'2C complex as well as with RecA itself in forming the catalytically active nucleofilament. Attempts to locate the respective interaction sites have been advanced in order to understand the various functions of RecA. An intriguing question is how these numerous functional sites are contained within this rather small protein (38 kDa). To assess more clearly the roles of the respective sites and to what extent the sites may be interacting with each other, we review and compare the results obtained from various biological, biochemical and physico-chemical approaches. From a three-dimensional model it is concluded that all sites are concentrated to one part of the protein. As a consequence there are significant overlaps between the sites and it is speculated that corresponding interactions may play important roles in regulating RecA activities.

Evolutionary conservation of RecA genes in relation to protein structure and function

Functional and structural regions inferred from the Escherichia coli R ecA protein crystal structure and mutation studies are evaluated in terms of evolutionary conservation across 63 RecA eubacterial sequences. Two paramount segments invariant in specific amino acids correspond to the ATP-binding A site and the functionally unassigned segment from residues 145 to 149 immediately carboxyl to the ATP hydrolysis B site. Not only are residues 145 to 149 conserved individually, but also all three-dimensional structural neighbors of these residues are invariant, strongly attesting to the functional or structural importance of this segment. The conservation of charged residues at the monomer-monomer interface, emphasizing basic residues on one surface and acidic residues on the other, suggests that RecA monomer polymerization is substantially mediated by electrostatic interactions. Different patterns of conservation also allow determination of regions proposed to interact with DNA, of LexA binding sites, and of filament-filament contact regions. Amino acid conservation is also compared with activities and properties of certain RecA protein mutants. Arginine 243 and its strongly cationic structural environment are proposed as the major site of competition for DNA and LexA binding to RecA. The conserved acidic and glycine residues of the disordered loop L1 and its proximity to the RecA acidic monomer interface suggest its involvement in monomer-monomer interactions rather than DNA binding. The conservation of various RecA positions and regions suggests a model for RecA-double-stranded DNA interaction and other functional and structural assignments.

Analysis of the DNA binding site of Escherichia coli RecA protein

To investigate the DNA binding site of RecA protein, we constructed 15 recA mutants having alterations in the regions homologous to the other ssDNA binding proteins. The in vivo analyses showed that the mutational change at Arg243, Lys248, Tyr264, or simultaneously at Lys6 and Lys19, or Lys6 and Lys23 caused severe defects in the recA functions, while other mutational changes did not. Purified RecA-K6A-K23A (Lys6 and Lys23 changed to Ala and Ala, respectively) protein was indistinguishable from the wild-type RecA protein in its binding to DNA. However, the RecA-R243A (Arg243 changed to Ala) and RecA-Y264A (Tyr264 changed to Ala) proteins were defective in binding to both ss- and ds-DNA. In self-oligomerization property, RecA-R243A was proficient but RecA-Y264A was deficient, suggesting that the RecA-R243A protein had a defect in DNA binding site and the RecA-Y264A protein was defective in its interaction with the adjacent RecA molecule. The region of residues 243-257 including the Arg243 is highly homologous to the DNA binding motif in the ssDNA binding proteins, while the eukaryotic RecA homologues have a similar structure at the amino-terminal side proximal to the nucleotide binding core. The region of residues 243-257 would be a part of the DNA binding site. The other parts of this site would be the Tyr103 and the region of residues 178-183, which were cross-linked to ssDNA. These three regions lie in a line in the crystal structure.

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.