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RecA

RecA is a multifunctional recombinase protein primarily found in bacteria, such as Escherichia coli, where it facilitates homologous DNA recombination, repairs double-strand breaks, and activates the SOS response to DNA damage by forming nucleoprotein filaments on single-stranded DNA (ssDNA).^[1] Discovered in 1965 through genetic screens identifying recombination-deficient mutants, RecA binds ssDNA in an ATP-dependent manner to search for homologous sequences, invade double-stranded DNA (dsDNA), and promote strand exchange, thereby restoring genome integrity during replication fork stalling or lesions.^[2]^[3] Structurally, RecA is a 38 kDa monomer composed of 352 amino acids, featuring a conserved core domain (residues 34–269) with ATP-binding Walker A and B motifs, an N-terminal domain for dsDNA interaction, and a less conserved, negatively charged C-terminal domain that modulates dsDNA binding and autoregulates activity.^[1]^[3] In its active form, RecA polymerizes into right-handed helical filaments with approximately six monomers per turn, a 95 Å pitch, and three nucleotides bound per monomer, extending ssDNA by 150–160% to facilitate homology recognition via transient base-flipping and minor groove interactions.^[1]^[4] This filament structure enables RecA's ATPase activity, which powers dynamic assembly and disassembly in a 5' to 3' direction, ensuring efficient DNA pairing without requiring ATP hydrolysis for the strand exchange step itself.^[3]^[4] In homologous recombination, RecA initiates repair by loading onto ssDNA exposed at replication forks or breaks, often mediated by accessory proteins like RecBCD (which recognizes Chi sites for loading) or the RecFOR pathway (which nucleates filaments on single-strand binding protein-coated ssDNA).^[1]^[5] The presynaptic filament then performs a homology search, forming a D-loop via 3' end invasion, followed by branch migration to create a Holliday junction resolved by resolvases like RuvABC.^[3] Beyond recombination, RecA's coprotease function is pivotal: ATP-bound RecA-ssDNA filaments facilitate the autocleavage of the LexA repressor, derepressing over 40 SOS genes—including those for error-prone polymerases like Pol V—to enable translesion synthesis and mutagenesis as a last-resort repair mechanism.^[4]^[3] RecA activity is tightly regulated at multiple levels to prevent inappropriate recombination or excessive mutagenesis.^[5] Transcriptionally, recA expression is SOS-inducible, with basal levels sufficient for routine repair.^[5] Post-translationally, the C-terminal domain inhibits spontaneous filament formation, while proteins like DinI stabilize filaments during SOS, RecX limits extension to prevent off-target effects, and UvrD helicase disassembles them post-repair.^[5]^[3] Single-strand binding protein (SSB) competes for ssDNA but is displaced by RecA nucleation, and inhibitors like RdgC block dsDNA access to fine-tune specificity.^[5] Homologs like RadA in archaea and Rad51 in eukaryotes share structural and functional similarities, underscoring RecA's evolutionary conservation in genome maintenance.^[1]

Discovery and historical context

Initial identification

The initial identification of RecA arose from genetic screens for recombination-deficient mutants in Escherichia coli K-12 during the mid-1960s. A. J. Clark and A. D. Margulies employed a bacterial conjugation assay, in which an Hfr donor strain transferred chromosomal markers to an F⁻ recipient, followed by penicillin enrichment to select against non-recombinants. This approach isolated several rec mutants that exhibited recombination frequencies reduced by over 1,000-fold compared to wild-type strains, indicating a critical role for these genes in homologous recombination. These recA mutants also demonstrated pronounced sensitivity to ultraviolet (UV) light, with survival fractions dropping to less than 10⁻⁴ after a 20 J/m² dose, in contrast to wild-type cells that retained over 10% viability under the same conditions. Complementation tests using partial diploids confirmed that the recA locus was responsible for both the recombination defect and UV sensitivity, establishing an early link between RecA function and DNA repair. In the 1970s, genetic mapping positioned the recA gene at approximately 58 minutes on the E. coli chromosome, and complementation experiments with cloned DNA fragments restored wild-type recombination proficiency in mutant backgrounds. The gene product was identified as a 38,000 Da protein, initially termed protein X, through radiochemical labeling of proteins induced after UV treatment in strains carrying a recA-transducing phage. Purification from overproducing strains via ion-exchange chromatography yielded a homogeneous protein that complemented recA defects in vivo. Early biochemical assays in the late 1970s revealed that purified RecA binds single-stranded DNA with high affinity in the presence of ATP, forming nucleoprotein filaments essential for recombination. In recombination-deficient strains, addition of exogenous RecA restored ATP-dependent DNA renaturation activity, where complementary single strands formed duplex aggregates at rates exceeding 10 times background levels when Mg²⁺ and ATP were provided. These findings solidified RecA's direct involvement in ATP-coupled DNA strand exchange.^[6]

Nomenclature and evolutionary conservation

The recA gene in Escherichia coli derives its name from "recombination," reflecting its identification as the first locus (denoted "A") associated with recombination-deficient mutants in early genetic screens.^[7] In initial studies, mutations in this gene were characterized for their defects in conjugal recombination and sensitivity to DNA-damaging agents.^[7] Early literature also referred to recA and its mutants by alternative designations, such as tif (for thermal induction of filamentation), lexB, or sbcA, highlighting its multifaceted roles beyond recombination, including in the SOS response and filamentation under stress.^[8] RecA exhibits strong evolutionary conservation across prokaryotes, being nearly ubiquitous in bacteria where it serves essential functions in DNA repair and homologous recombination, with a single recA gene per genome in most eubacterial species.^[9] Core domains, including the DNA-binding L1 and L2 loops, are highly preserved, featuring conserved acidic and glycine residues that facilitate monomer interactions and DNA engagement during filament formation.^[10] However, recA is absent in some bacteria with highly reduced minimal genomes, such as certain obligate intracellular parasites like Mycoplasma species, which rely on alternative recombination pathways.^[11] Phylogenetic analyses frequently employ RecA as a reliable molecular marker for bacterial taxonomy, as its sequences reveal deep evolutionary relationships and enable subclassification of major groups.^[12] For instance, within the gamma-proteobacteria, RecA proteins share sequence identities often exceeding 50%, supporting distinctions between ecologically divergent subgroups like those associated with vertebrate hosts versus soil environments.^[12] Key conserved residues, such as those in the Walker A and B motifs for ATP binding and hydrolysis, have been pinpointed through multiple sequence alignments, underscoring their functional invariance across diverse bacterial lineages.^[10]

Structural features

Monomer architecture

The RecA monomer from Escherichia coli is a single polypeptide chain of 353 amino acids with a molecular weight of 37.8 kDa (approximately 38 kDa).^[8] It adopts a compact fold comprising three distinct domains: an N-terminal domain spanning residues 1–33, which plays a regulatory role in protein interactions; a central core domain encompassing residues 34–269, responsible for ATPase activity; and a C-terminal domain covering residues 270–353, which facilitates interactions with DNA and accessory proteins.^[13]^[14] The central domain exhibits a characteristic RecA fold, featuring a seven-stranded β-sheet flanked by α-helices and an α-helical bundle that contributes to nucleotide binding. Two prominent flexible loops extend from this domain: loop L1 (residues 157–164) and loop L2 (residues 195–209), which are disordered in the crystal structure but are crucial for gripping single-stranded DNA through direct contacts.^[13] These elements position the monomer for assembly into higher-order structures while maintaining functional versatility. The atomic structure of the RecA monomer was first determined in 1992 by Story et al. using X-ray crystallography at 2.3 Å resolution (PDB: 2REB), revealing the nucleotide-free (apo) form with a modeled ADP-binding site in the core domain.^[13]

Filament assembly and dynamics

RecA monomers assemble into a right-handed helical nucleoprotein filament on single-stranded DNA (ssDNA), a process essential for homologous recombination. This assembly begins with nucleation, where cooperative binding of 3-6 RecA monomers to ssDNA overcomes an initial energy barrier, facilitated by the protein's core domain interactions that promote multimerization. Once nucleated, the filament extends directionally, with monomers adding primarily to the 3' end relative to the ssDNA polarity, forming a continuous helix comprising approximately 6 monomers per turn and a pitch of 95 Å. The polymerization involves the central core domain of RecA monomers interfacing with adjacent subunits, as briefly noted in structural descriptions of the monomer architecture. The filament exhibits structural transitions between active and inactive states tied to nucleotide binding. In the ATP-bound conformation, the filament adopts an extended helical structure (pitch ~95-100 Å), which is competent for DNA binding and recombination activities. In contrast, the ADP-bound state compresses the helix (pitch ~74 Å), rendering it inactive and prone to disassembly. These transitions occur dynamically, with filaments reversibly interconverting between states, and the compressed form occasionally exhibiting variable handedness, including a roughly 50% occurrence of left-handed configurations in certain conditions.^[15] Filament dynamics involve treadmilling, where RecA monomers dissociate from the 5' proximal end while adding to the 3' end, maintaining filament length under steady-state conditions despite ATP hydrolysis. This process is influenced by single-stranded DNA-binding protein (SSB), which initially coats ssDNA but is displaced by incoming RecA during nucleation and extension, with SSB diffusion aiding RecA access to binding sites. In vivo, RecA filaments can reach lengths corresponding to up to 10 kb of ssDNA, enabling efficient homology search across large genomic regions. Recent cryo-electron microscopy (cryo-EM) studies have provided high-resolution insights into the presynaptic filament structure. For instance, the 2023 structure of the Streptococcus pneumoniae RecA-ssDNA filament (PDB: 8AMD) reveals the helical arrangement at 3.9 Å resolution, highlighting how the L1 and L2 loops of RecA protrude to engage ssDNA in the active extended state, consistent with earlier E. coli models but refined for bacterial diversity. Similarly, 2023 cryo-EM structures of E. coli RecA filaments in complex with SOS regulators like DinI and LexA (e.g., PDB: 8F0R) illustrate how these proteins modulate filament assembly and stability.^[16]^[17]

Biochemical mechanisms

DNA binding and strand exchange

RecA exhibits two distinct DNA-binding sites that facilitate its role in homologous recombination. The primary binding site interacts with high affinity to single-stranded DNA (ssDNA), with a dissociation constant (K_d) of approximately 10 nM, primarily through the flexible L1 and L2 loops located in the core domain of the RecA monomer.^[18]^[19] These loops enable cooperative binding, encircling the ssDNA in a right-handed helical nucleoprotein filament with a stoichiometry of about three nucleotides per RecA monomer.^[20] In contrast, the secondary binding site shows lower affinity for double-stranded DNA (dsDNA), typically in the range of 10- to 100-fold weaker than for ssDNA, and is mediated by the C-terminal domain, which initially captures dsDNA during homology search.^[21] This differential affinity ensures preferential filament formation on ssDNA as a prerequisite for subsequent interactions.^[22] The strand exchange mechanism promoted by RecA involves a three-strand exchange process where the RecA-ssDNA filament invades a homologous dsDNA molecule. In the presynapsis phase, the nucleoprotein filament assembles on ssDNA, stretching it to a 1.5-fold extended conformation suitable for homology recognition.^[20] Synapsis follows, during which the secondary site binds incoming dsDNA, and the L2 loop inserts into the duplex to unwind it base-pair by base-pair, allowing the homologous ssDNA strand to pair and form an initial 10-12 base pair heteroduplex while displacing the non-complementary strand to create a displacement loop (D-loop).^[22] Branch migration then extends the heteroduplex region unidirectionally, driven by sequential ATP binding and hydrolysis, propagating the exchange over thousands of base pairs.^[21] Key intermediates in this process include paranemic joints, where the ssDNA and dsDNA align in parallel without interwinding or base pairing, facilitating initial homology sampling, and plectonemic joints, which form as the strands intertwine during branch migration, stabilizing the exchanged structure.^[22] The transition from paranemic to plectonemic configurations involves a 5'-directed tilt in the invading strand initially, shifting to 3'-directed progression for termination.^[20] In vitro assays reconstitute RecA-mediated strand exchange using circular ssDNA (e.g., phage φX174) coated with RecA and linear homologous dsDNA, yielding D-loop or Holliday junction intermediates detectable by gel electrophoresis.^[23] Post-exchange, these Holliday junctions require RuvAB for efficient branch migration and RecA filament disassembly, followed by RuvC resolution to produce recombinant products, achieving up to 65% yield in optimized systems.^[23]

ATPase activity and energy coupling

RecA exhibits DNA-dependent ATPase activity, hydrolyzing ATP to ADP and inorganic phosphate (P_i) in a manner tightly coupled to its role in homologous recombination. In the absence of DNA, RecA displays a low basal ATPase rate of approximately 0.02 min⁻¹ per monomer, with a K_m for ATP around 60 μM under neutral pH conditions.^[24] This activity is dramatically stimulated by single-stranded DNA (ssDNA), increasing the turnover number (k_cat) to 20–30 ATP hydrolyzed per minute per RecA monomer, representing a roughly 1000-fold enhancement.^[25]^[24] The Michaelis-Menten parameters under these conditions show a K_m for ATP of approximately 20–50 μM, indicating high affinity, and the reaction follows cooperative kinetics with a Hill coefficient of about 3, reflecting the multimeric nature of the RecA filament.^[24]^[26] The ATPase cycle is integral to RecA's functional dynamics within the nucleoprotein filament. ATP binding to RecA monomers promotes assembly into an active, extended helical conformation that enhances ssDNA affinity and facilitates presynaptic complex formation, as well as initial strand invasion during homology search.^[22] Subsequent ATP hydrolysis, stimulated by ssDNA binding, powers the unidirectional branch migration phase of strand exchange, where the invading strand extends through the homologous duplex at a rate of approximately 20 base pairs per ATP molecule hydrolyzed.^[27] This hydrolysis also drives partial filament disassembly, allowing dynamic turnover of RecA monomers to prevent stagnation and support processive recombination over long DNA stretches.^[26] The simplified reaction for filament-associated hydrolysis can be represented as:

\text{RecA}_{6n} + n \text{ ATP} + \text{ssDNA} \rightarrow \text{RecA}_{6n} \cdot \text{ssDNA} + n \text{ ADP} + n \text{ P}_i

where the subscript denotes the hexameric repeat unit of the filament, and n scales with filament length.^[26] Nucleotide analogs modulate this ATPase activity by trapping specific conformational states. The non-hydrolyzable ATP analog AMPPNP binds tightly and stabilizes the active filament conformation, promoting DNA binding and presynaptic filament formation but inhibiting hydrolysis-dependent steps like branch migration.^[22] In contrast, ADP favors the inactive, compressed filament state, reducing DNA affinity and ATPase stimulation, thereby acting as a competitive inhibitor with respect to ATP.^[24] These regulatory effects underscore the energy coupling that links nucleotide state to RecA's mechanochemical cycle.

Biological roles in bacteria

Homologous recombination and DNA repair

RecA plays a central role in bacterial homologous recombination, particularly in the repair of double-strand breaks (DSBs), which arise from replication fork collapse, ionizing radiation, or other genotoxic stresses. In Escherichia coli, the primary pathway for DSB repair begins with the RecBCD helicase-nuclease complex binding to the broken DNA ends. RecBCD unwinds and resects the duplex DNA in a 5' to 3' direction, generating a 3' single-stranded DNA (ssDNA) tail, until it encounters a Chi (crossover hotspot instigator) sequence, typically 5'-GCTGGTGG-3'. At Chi sites, RecBCD's nuclease activity attenuates, and it facilitates the loading of RecA onto the ssDNA, forming a right-handed helical nucleoprotein filament. This RecA-ssDNA filament then searches for and invades a homologous duplex region, often on the sister chromosome, initiating strand exchange to restore the broken chromosome through gene conversion or other outcomes.^[28]^[29]^[30] Beyond DSBs, RecA contributes to the repair of other replication-associated lesions. In post-replication gap repair, UV-induced pyrimidine dimers or other blocks stall the replication fork, leaving ssDNA gaps in the daughter strand. RecA binds these gaps, often with assistance from the RecFOR pathway, and promotes recombination with the continuous sister duplex to fill the gap via template-directed synthesis, preventing fork collapse into a DSB. Similarly, interstrand crosslinks (ICLs), formed by agents like psoralen or mitomycin C, block replication and transcription; initial unhooking by nucleotide excision repair (e.g., UvrABC) generates a DSB-like intermediate, which RecA resolves through recombination-dependent bypass, ensuring genome continuity. These processes highlight RecA's versatility in tolerating and repairing replication stress without triggering error-prone alternatives.^[31]^[32]^[33] Genetic studies underscore RecA's essentiality in these pathways. Mutations in recA result in a dramatic reduction (often >1,000-fold) in homologous recombination frequency, rendering cells hypersensitive to DNA-damaging agents like UV light and ionizing radiation.^[34] Furthermore, recA mutants exhibit severe synthetic sickness when combined with recBCD mutations under genotoxic conditions, as the absence of RecBCD prevents ssDNA generation for RecA loading, leading to unrepaired DSBs and poor viability. These phenotypes confirm RecA's indispensable role in recombination-mediated repair.^[35]^[36] Two main models describe RecA-dependent DSB repair in bacteria: the double-strand break repair (DSBR) model and synthesis-dependent strand annealing (SDSA). In DSBR, after RecA-mediated invasion by one DSB end, the second end is captured to form a double Holliday junction, which is resolved by RuvABC, potentially yielding crossovers that exchange flanking markers. In contrast, SDSA involves only one end invading the homolog, with DNA polymerase extending the invading strand before it anneals back to the original DSB end, favoring non-crossover gene conversion and avoiding crossovers, which is predominant in mitotic-like bacterial growth. The core strand exchange step in both models relies on RecA's ability to align and pair homologous sequences.^[37]^[38]

SOS response induction

The SOS response in bacteria, such as Escherichia coli, is triggered by DNA damage that generates single-stranded DNA (ssDNA), which serves as a signal for RecA activation.^[39] Upon binding to ssDNA in the presence of ATP, RecA forms a nucleoprotein filament that adopts an extended conformation, enabling its coprotease activity.^[40] This activated RecA filament, often denoted as RecA*, facilitates the autocleavage of the LexA repressor protein, a key regulator that normally binds to SOS box operators in promoter regions to repress transcription.^[41] The seminal discovery of RecA's role as a coprotease in promoting LexA cleavage was reported in 1980, establishing the mechanism by which DNA damage induces the SOS regulon.^[41] The interaction between RecA* and LexA positions the repressor's cleavage site—a specific Ala84-Gly85 peptide bond within its C-terminal domain—adjacent to LexA's own catalytic Ser119-Lys156 dyad, accelerating the intramolecular hydrolysis reaction by several orders of magnitude compared to unstimulated LexA.^[42] This self-cleavage inactivates LexA dimers, leading to their dissociation from DNA and derepression of over 50 SOS genes involved in DNA repair, cell division inhibition, and mutagenesis.^[43]^[44] Efficient coprotease activity requires an extended RecA filament of sufficient length, typically involving multiple RecA protomers (with studies indicating that filaments spanning at least several hundred nucleotides of ssDNA are optimal for robust LexA stimulation, corresponding to over 100 RecA monomers given the ~3 nucleotides covered per monomer).^[40] In vivo, this threshold ensures that SOS induction occurs only when significant ssDNA accumulation signals substantial DNA damage, with full activation typically observed 5-10 minutes post-damage in UV-irradiated cells.^[45] A major outcome of LexA cleavage is the upregulation of error-prone DNA polymerases, such as DNA polymerase V (Pol V, encoded by umuDC), which enables translesion synthesis across damaged templates but at the cost of increased mutation rates.^[46] Pol V activity is particularly dependent on RecA*, as the polymerase incorporates RecA as a subunit in its mutasomal complex (Pol V Mut = UmuD'₂C-RecA-ATP), facilitating replication bypass and contributing to SOS-induced mutagenesis.^[47] This mutagenic pathway enhances survival under genotoxic stress but promotes genetic variability, including adaptive mutations.^[46] The SOS response includes positive feedback on RecA expression, as the recA gene itself is under LexA repression; upon induction, RecA protein levels increase 10- to 20-fold within minutes, amplifying filament formation and sustaining the response until DNA damage is resolved.^[48] This autoregulatory loop ensures rapid and proportional escalation of repair mechanisms proportional to damage severity.^[49]

Involvement in genetic exchange

Natural competence and transformation

Natural competence is a physiological state in certain bacteria that enables the uptake of exogenous DNA from the environment, typically as single-stranded DNA (ssDNA), which is then integrated into the genome through homologous recombination. In species like Bacillus subtilis, this process occurs primarily during stationary phase in a subpopulation of cells, where the incoming ssDNA is protected and loaded with RecA to form nucleoprotein filaments that search for homologous sequences on the chromosome, initiating strand invasion and D-loop formation for stable integration.^[50]^[51] RecA is essential for the recombinational integration step, as it polymerizes on the ssDNA to facilitate homology recognition and strand exchange; without RecA, the incoming DNA is degraded rather than incorporated. In Streptococcus pneumoniae, recA mutants exhibit transformation efficiencies reduced by approximately 30-fold compared to wild-type cells, demonstrating strong dependence on RecA for producing transformants.^[52] Similarly, in B. subtilis, chromosomal transformation efficiency in ΔrecA mutants drops to less than 0.01% of wild-type levels, a reduction exceeding 10,000-fold, while plasmid transformation remains largely unaffected, highlighting RecA's specific role in homologous chromosomal integration.^[53]^[51] The requirement for RecA varies slightly across species but is universally critical for transformation. In S. pneumoniae, RecA is upregulated as part of the competence regulon, ensuring sufficient levels for efficient recombination during transient competence induced by stress or high density. In contrast, Neisseria gonorrhoeae maintains constitutive competence without RecA induction, yet recA mutants show substantially reduced transformation efficiency, underscoring RecA's indispensable role in ssDNA integration even in continuously competent cells.^[52]^[50]^[54] Experimental evidence from transformation assays confirms these dependencies. In S. pneumoniae, competence assays using recA knockout strains and fluorescence microscopy reveal no formation of RecA-DprA foci at replication forks upon ssDNA addition, correlating with abolished transformation; wild-type cells show rapid filament assembly and substantially higher integration rates. In B. subtilis, marker rescue assays with ΔrecA strains demonstrate blocked chromosomal recombination, with efficiencies below detection limits for homologous markers, while heterologous DNA uptake proceeds but fails to integrate without RecA-mediated strand exchange. These studies collectively establish RecA's promotion of D-loop formation as the key bottleneck in transformation success.^[55]^[56]^[51]

Conjugation and plasmid transfer

In bacterial conjugation, the Tra machinery of conjugative plasmids, such as the F-plasmid, exports single-stranded DNA (ssDNA) from the donor cell to the recipient through a type IV secretion system. Upon arrival in the recipient cytoplasm, the ssDNA is initially bound by single-stranded DNA-binding protein (SSB) to prevent degradation. If homologous sequences are present in the recipient genome, RecA polymerizes onto this ssDNA to form a helical nucleoprotein filament. This RecA-ssDNA filament promotes single-strand invasion, initiating homologous recombination that allows the transferred DNA to pair with homologous regions, such as resident plasmids or the chromosome.^[57] The RecA-mediated strand invasion is critical for resolving cointegrates that arise during plasmid transfer when homology leads to recombination, forming multimers. These cointegrates are subsequently resolved by the host's XerCD site-specific recombinase at dif sites, restoring monomeric plasmids or chromosomal structures for stable replication and segregation. Without RecA, homologous recombination is impaired, leading to unstable intermediates in cases of homology, though non-homologous plasmid establishment via autonomous replication can still occur. RecA's ATPase activity couples energy to filament dynamics, ensuring efficient invasion and exchange during this process.^[58]^[57] RecA's role in conjugation contributes to horizontal gene transfer (HGT) by facilitating recombination-dependent stabilization and dissemination of plasmids carrying virulence factors and antibiotic resistance genes. Studies with recA mutants demonstrate defects in recombination and integration of transferred DNA when homology is present. This underscores RecA's contribution to the evolutionary success of conjugative plasmids in promoting adaptive genetic exchange, particularly in homologous contexts.^[59] In the F-plasmid system, RecA facilitates the RecE recombination pathway, an alternative RecA-dependent mechanism encoded by the Rac prophage that enhances strand exchange during transfer. Although the F-plasmid encodes the PsiB inhibitor to modulate RecA activity and suppress SOS response induction by the incoming ssDNA, RecA remains essential for homology-directed integration and plasmid establishment in the recipient when recombination is required. Directed evolution experiments have produced RecA variants (e.g., V79L, I102L) that increase F-plasmid conjugation efficiency by 2.5- to 3-fold through improved filament stability and reduced sensitivity to regulators like RecX, confirming RecA as a key factor in recombination-limited steps of this process.^[60]^[57]

Homologs and comparative biology

Eukaryotic counterparts (Rad51 family)

In eukaryotes, the primary functional counterpart to the bacterial RecA protein is Rad51, a recombinase that shares approximately 30% sequence identity with Escherichia coli RecA in its core ATPase domain.^[61] Both proteins assemble into right-handed helical nucleoprotein filaments on single-stranded DNA (ssDNA), with each monomer binding about three nucleotides, to search for homologous sequences and promote strand invasion during recombination.^[61] However, Rad51 filaments are more dynamic and exhibit irregular pitch and subunit rotation compared to the highly ordered structure of RecA filaments, reflecting adaptations to the complex eukaryotic chromatin environment.^[62] Unlike RecA, which binds ssDNA autonomously, Rad51 requires mediator proteins such as BRCA2 to displace replication protein A (RPA) and nucleate filaments on RPA-coated ssDNA, ensuring efficient presynaptic assembly.^[62] Functionally, Rad51 drives double-strand break (DSB) repair and meiotic recombination via the homologous recombination (HR) pathway, invading homologous duplex DNA to form displacement loops (D-loops) that enable error-free repair using the sister chromatid as a template.^[62] This process is tightly regulated in the S and G2 phases of the cell cycle to maintain genome stability. Rad51 activity is inhibited by anti-recombinases like RADX, which binds ssDNA and caps Rad51 filaments to prevent excessive extension and promote timely disassembly, thereby balancing recombination with replication fork progression.^[63] Key differences from RecA include the absence of coprotease activity in Rad51, which in bacteria facilitates LexA cleavage for the SOS response but is not conserved in eukaryotes, and enhanced fidelity in strand exchange due to Rad51's preference for unidirectional invasion from the 3' end of ssDNA overhangs.^[61] Additionally, Rad51's ATPase activity is significantly lower (0.16–0.21 ATP/min) than RecA's, supporting controlled filament dynamics rather than rapid turnover.^[61] Mutations in RAD51 compromise HR efficiency and are linked to genomic instability and disease. Heterozygous dominant-negative variants cause Fanconi anemia complementation group R (FANCR), characterized by defective DSB repair, bone marrow failure, and cancer predisposition due to impaired filament stability and fork protection.^[64] RAD51 also interacts with BRCA1 and BRCA2, and its dysregulation exacerbates breast and ovarian cancer risk, as seen in variants that disrupt mediator recruitment and HR fidelity.^[62] These links highlight Rad51's critical role in suppressing tumorigenesis through precise recombination.

Archaeal and viral RecA-like proteins

Archaeal RecA homologs, primarily known as RadA proteins, play essential roles in homologous recombination and DNA repair, sharing approximately 20-30% amino acid sequence identity with bacterial RecA while exhibiting higher similarity (around 40%) to eukaryotic Rad51 proteins.^[65]^[66] In hyperthermophilic archaea such as Sulfolobus solfataricus, RadA catalyzes ATP-dependent DNA strand exchange, forming joint molecules between single-stranded and double-stranded DNA substrates at elevated temperatures (e.g., 65–90°C), which supports repair in extreme thermal environments.^[65]^[67] These proteins assemble into right-handed helical nucleoprotein filaments on single-stranded DNA, with a pitch of about 10.6 nm and one monomer binding every three nucleotides, facilitating homologous pairing analogous to RecA's mechanism.^[65] RadA filaments in archaea like Sulfolobus exhibit structural adaptations for stability in hyperthermophilic conditions, maintaining activity across a broad temperature range (37-90°C) and showing enhanced thermostability compared to bacterial RecA. In halophilic archaea, such as those in the genus Haloferax, RadA variants tolerate high intracellular salt concentrations (near saturation levels of KCl), enabling function in hypersaline habitats through acid-enriched surface residues that prevent aggregation under ionic stress. These adaptations underscore RadA's role in preserving genomic integrity amid environmental extremes, with knockout studies in Sulfolobus islandicus revealing increased sensitivity to DNA-damaging agents like UV radiation. A key accessory to RadA is the paralog RadB, found predominantly in euryarchaea, which functions as a recombination mediator by stimulating RadA's strand exchange activity without possessing significant ATPase or strand exchange capabilities itself. RadB interacts directly with RadA to load it onto single-stranded DNA, analogous to bacterial accessory proteins like RecFOR or eukaryotic Rad52, and genetic analyses in Haloferax volcanii demonstrate that RadB mutants exhibit recombination defects that are suppressed by RadA overexpression. Viral RecA-like proteins, such as UvsX in bacteriophage T4, share approximately 23% sequence identity with bacterial RecA and are critical for recombination-dependent DNA replication during infection.^[68]^[69] UvsX forms helical filaments on single-stranded DNA, promoting homologous pairing and strand invasion, while displacing the phage single-stranded DNA-binding protein gp32 to initiate replication forks; this process is essential for generating concatemeric genomes from terminally redundant ends.^[68] In T4, UvsX-mediated recombination supports rapid progeny production, contributing to high burst sizes (up to 200-300 virions per cell) by enabling efficient repair and replication under host stress. These archaeal and viral RecA homologs highlight evolutionary divergences from bacterial RecA, with RadA and Rad51 forming a clade distinct from RecA, suggesting their common origin in the last universal common ancestor (LUCA) through ancient gene duplication events that predated the split of bacterial, archaeal, and eukaryotic lineages. This ancestral recombinase likely facilitated primordial DNA repair, with subsequent adaptations enabling specialization in extremophiles and viral life cycles.

Applications and significance

Clinical relevance in antibiotic resistance

RecA plays a central role in the development of antibiotic resistance through its activation of the SOS response, which promotes error-prone DNA repair and mutagenesis in bacteria exposed to DNA-damaging antibiotics. When antibiotics like fluoroquinolones induce DNA double-strand breaks, RecA filaments form on single-stranded DNA, facilitating the autocleavage of the LexA repressor and derepressing SOS genes, including those encoding low-fidelity polymerases such as Pol V. This leads to hypermutation rates, enabling the rapid evolution of resistance mutations in target genes like gyrA and parC, which encode DNA gyrase and topoisomerase IV, respectively.^[70]^[71]^[72] In specific pathogens, RecA contributes to resistance via mechanisms like gene amplification. For instance, in Pseudomonas aeruginosa, RecA-dependent tandem amplification of the beta-lactamase gene blaSHV-5 generates heteroresistant subpopulations with elevated enzyme copy numbers, conferring high-level resistance to beta-lactams such as ceftazidime; deletion of recA abolishes this amplification under antibiotic pressure.^[73] Similarly, RecA inhibition has been shown to reduce bacterial persistence, the tolerant subpopulation that survives antibiotic treatment without genetic resistance, by disrupting SOS-mediated survival pathways in P. aeruginosa biofilms.^[74] Therapeutic strategies targeting RecA aim to sensitize bacteria to antibiotics and prevent resistance evolution. Small-molecule RecA inhibitors, such as iron(III) phthalocyanine-4,4′,4″,4‴-tetrasulfonic acid (Fe-PcTs), block RecA filamentation and ATPase activity, synergizing with fluoroquinolones and beta-lactams to potentiate killing in Gram-negative bacteria including P. aeruginosa; in murine models of infection, Fe-PcTs co-administration eliminated resistant subpopulations. Other compounds, like 2-aminoimidazole derivatives, similarly inhibit RecA and reduce mutagenesis rates, though as of 2025, no RecA inhibitors have advanced to clinical trials for multidrug-resistant (MDR) infections, with efforts focused on preclinical optimization for synergy against MDR pathogens.^[75]^[76] RecA-mediated resistance exacerbates the global burden of antimicrobial resistance (AMR), which is attributable to bacterial AMR caused over 1.20 million deaths annually as of 2019, with projections estimating up to 1.91 million by 2050 if unchecked.^[77] This impact underscores RecA's role as a high-value target for interventions to curb the spread of MDR infections.

Biotechnological and synthetic biology uses

RecA plays a pivotal role in biotechnological applications, particularly in recombineering techniques for bacterial genome engineering. In Escherichia coli, the lambda Red system, which facilitates RecA-independent homologous recombination, has been augmented by transient co-expression of RecA to enhance recombination efficiency, especially for editing large constructs like bacterial artificial chromosomes (BACs). This approach improves host cell survival during transformation and increases the yield of successful recombinants using either double- or single-stranded DNA donors, enabling precise insertions, deletions, and modifications with minimal off-target effects.^[78] In synthetic biology, RecA-based genetic circuits serve as sensitive DNA damage sensors within biosensors for detecting genotoxic agents. Engineered promoters from the RecA regulon, such as the Vibrio natriegens P_VRecA variant redesigned with an AT-rich spacer (P_VRecA-AT), exhibit ultrasensitive responses to stressors like UV radiation and mitomycin C, achieving up to a 128-fold induction of reporter genes over extended periods. These circuits incorporate amplifiers and feedback loops for robustness against environmental variations, allowing applications in environmental monitoring and cellular diagnostics. Additionally, the UV-inducible nature of RecA filament formation enables optogenetic-like control, where spatial activation via targeted light exposure triggers SOS responses in engineered cells without chemical inducers.^[79] For industrial applications, RecA's eukaryotic homolog Rad51 has been overexpressed in yeasts like Pichia pastoris to boost homologous recombination efficiency, facilitating metabolic engineering. Overexpression of PpRAD51 increases the success rate of seamless gene deletions and multi-gene integrations to approximately 12.5%, compared to near-zero in wild-type strains, by enhancing strand invasion during repair. This has enabled the construction of pathways for producing high-value compounds, such as fatty alcohols at yields of 12.6–380 mg/L, by integrating enzymes at neutral genomic loci under optimized promoters.^[80] Recent advances include CRISPR-Cas9 fusions with RecA or its homologs to promote precise homologous recombination while minimizing non-homologous end joining (NHEJ). For instance, Cas9-RecA fusion proteins have been shown to enhance single-strand annealing (SSA), a form of HR, by 2.5-fold in human HEK293T cells, improving targeted edits for gene therapy applications.^[81]

References

[1]
RecA: Regulation and Mechanism of a Molecular Search Engine - NIH
Here, we review the regulation of RecA filament assembly and the mechanism by which RecA quickly and efficiently searches for and identifies a unique homologous ...
[2]
ISOLATION AND CHARACTERIZATION OF RECOMBINATION ...
ISOLATION AND CHARACTERIZATION OF RECOMBINATION-DEFICIENT MUTANTS OF ESCHERICHIA COLI K12. ... Authors. A J CLARK, A D MARGULIES. PMID: 14294081; PMCID: PMC219534 ...Missing: recA sensitivity frequency assays
[3]
[PDF] THE BACTERIAL RECA PROTEIN AND THE RECOMBINATIONAL ...
(b) The RecA protein is required for the mutagenic bypass of DNA lesions during the SOS response, a reaction catalyzed by DNA polymerase V (37, 38). If the ...
[4]
Design and comparative characterization of RecA variants - Nature
Oct 26, 2021 · RecA plays a central role in DNA repair and is a main actor involved in recombination and activation of the SOS response.
[5]
Regulation of bacterial RecA protein function - PubMed - NIH
The RecA protein is a recombinase functioning in recombinational DNA repair in bacteria. RecA is regulated at many levels.
[6]
ATP-dependent renaturation of DNA catalyzed by the recA protein of ...
Incubation of the recA protein with complementary single strands of DNA, Mg2+, and ATP results in the rapid formation of large DNA aggregates containing many ...
[7]
ISOLATION AND CHARACTERIZATION OF RECOMBINATION-DEFICIENT MUTANTS OF ESCHERICHIA COLI K12* | PNAS
**Summary of recA Gene Naming from PNAS Article:**
[8]
Protein RecA - Escherichia coli (strain K12) | UniProtKB | UniProt
Jan 23, 2007 · Gene. recA ; Status. UniProtKB reviewed (Swiss-Prot) ; Organism. Escherichia coli (strain K12) ; Protein existence. Evidence at protein level.Missing: nomenclature origin
[9]
Origins and evolution of the recA/RAD51 gene family - PNAS
Jul 5, 2006 · The bacterial recA gene and its eukaryotic homolog RAD51 are important for DNA repair, homologous recombination, and genome stability.Results · Reca/rad51-Like Genes · Discussion<|control11|><|separator|>
[10]
Evolutionary conservation of RecA genes in relation to protein structure and function | Journal of Bacteriology
### Summary of Evolutionary Conservation of RecA
[11]
Comparative and Evolutionary Analysis of the Bacterial Homologous ...
Unsurprisingly, bacteria lacking RecA have very few other recombination proteins. ... Indeed, except for genomes lacking RecA and resolvases (which are stable ...
[12]
Bacterial classifications derived from recA protein sequence ... - NIH
Following this protocol, the gamma-proteobacteria can be subclassified into two major groups, those of mostly vertebrate hosts and those of mostly soil habitat.Missing: marker | Show results with:marker
[13]
The structure of the E. coli recA protein monomer and polymer - Nature
Jan 23, 1992 · The crystal structure of the recA protein from Escherichia coli at 2.3-Å resolution reveals a major domain that binds ADP and probably single- and double- ...
[14]
https://jbc.org/article/S0021-9258%2818%2980317-9/fulltext
[15]
The structure of the E. coli recA protein monomer and polymer
Jan 23, 1992 · The crystal structure of the recA protein from Escherichia coli at 2.3-A resolution reveals a major domain that binds ADP and probably single- and double- ...
[16]
Domain structure and dynamics in the helical filaments formed by ...
It can be seen that the lattice generated from the ADP-dsDNA-RecA filaments provides a very good match to the in situ crystal (b), but the ATP-dsDNA-filament ...
[17]
Assembly mechanism and cryoEM structure of RecA recombination ...
The initial atomic model of SpRecA protomers in both presynaptic and post-synaptic complexes were generated from the crystal structure of E. coli RecA (PDB ...
[18]
https://pubmed.ncbi.nlm.nih.gov/3888263/
[19]
https://doi.org/10.1038/355487a0
[20]
https://doi.org/10.1038/s41586-020-2820-9
[21]
https://doi.org/10.1093/emboj/17.4.1161
[22]
https://doi.org/10.1016/j.molcel.2008.03.010
[23]
https://doi.org/10.1016/S0092-8674(00)80242-1
[24]
Organized Unidirectional Waves of ATP Hydrolysis within a RecA ...
Waves of ATP hydrolysis move unidirectionally through RecA filaments on dsDNA, with successive waves occurring at intervals of approximately six monomers.
[25]
Properties of the duplex DNA-dependent ATPase activity of ... - PNAS
Elsewhere we demonstrate that the dsDNA-dependent ATPase activity is proportional to the rate of recA protein-catalyzed branch migration. We suggest that this ...
[26]
https://www.pnas.org/doi/10.1073/pnas.84.10.3127
[27]
RecA finds homologous DNA by reduced dimensionality search
Sep 1, 2021 · ... RecA filament is on different length scales in the cell. It appears to be flexible on the 100-nm length scale, but the probing interactions ...
[28]
Quantitative genomic analysis of RecA protein binding during DNA ...
In Escherichia coli, RecA-mediated homologous recombination plays an essential role in the repair of DNA double-strand breaks (DSBs). A greater understanding of ...
[29]
Chi hotspot control of RecBCD helicase-nuclease by long-range ...
Nov 5, 2020 · In many bacteria, including Escherichia coli studied here, the major pathway of homologous recombination and DNA break repair requires RecBCD ...
[30]
Generation and Repair of Postreplication Gaps in Escherichia coli
The formation of a RecA filament in the gap, a step often referred to as presynapsis, occurs with the aid of the RecF, RecO, and RecR proteins, in a variety of ...
[31]
The Bacterial RecA Protein and the Recombinational DNA Repair of ...
Jul 1, 2002 · RecA protein promotes DNA strand exchange, a reaction that contributes to fork regression and DNA end invasion steps.
[32]
Repair of DNA containing interstrand crosslinks in Escherichia coli
The repair of DNA containing interstrand crosslinks induced by psoralen-plus-light in E. coli cells has been investigated. During a 30-minute incubation ...
[33]
Acinetobacter baumannii RecA Protein in Repair of DNA Damage ...
At each UV light dose tested, the recA mutant was at least 1,000-fold ... In addition, homologous recombination was not detected in the recA mutant (Table 2).
[34]
Robust linear DNA degradation supports replication–initiation ...
RecBCD helicase/nuclease supports replication fork progress via recombinational repair or linear DNA degradation, explaining recBC mutant synthetic lethality.
[35]
Synthetic Lethality with the dut Defect in Escherichia coli Reveals ...
The synthetic lethality of dut mutations with all known mutations inactivating double-strand DNA break repair (recA, recBC, and ruvABC) (34) indicates that ...
[36]
Prevalent role of homologous recombination in the repair of specific ...
Feb 27, 2024 · A variation of this process, called synthesis-dependent strand annealing (SDSA), could also repair a DSB without needing a Holliday Junction.Introduction · Results · Discussion · Materials and methods
[37]
Homologous recombination in DNA repair and DNA damage tolerance
Jan 1, 2008 · A central core of proteins, most critically the RecA homolog Rad51, catalyzes the key reactions that typify HR: homology search and DNA strand ...
[38]
Separation of Recombination and SOS Response in Escherichia ...
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 ...Missing: seminal | Show results with:seminal
[39]
RecA-mediated SOS induction requires an extended filament ...
The double mutant protein will form long extended filaments on ssDNA and facilitate LexA cleavage almost as well as wild type, and do so in the presence of ATP.
[40]
Cleavage of the Escherichia coli lexA protein by the recA protease.
The recA and lexA proteins of EScherichia coli are involved in a complex regulatory circuit that allows the expression of a diverse set of functions after ...
[41]
RecA-Dependent Cleavage of LexA Dimers - PMC - NIH
SOS-inducing treatments activate another regulatory protein, RecA, which in turn inactivates LexA by a specific cleavage reaction, leading to de-repression of ...Introduction · Results · Discussion
[42]
Mutate or die: Atomic structures explain bacterial SOS induction
Jan 24, 2023 · Since the LexA protein is the repressor for recA and ~40 to 50 other genes, the cleavage of LexA inactivates its repressor function and induces ...
[43]
Kinetics of lexA and recA transcriptional activity following induction
The products of the lexA and recA genes play central roles in the regulation of the Escherichia coli SOS response. We have measured the rate of mRNA synthe.
[44]
Roles of DNA polymerases V and II in SOS-induced error ... - PNAS
pol V is able to copy UV-damaged DNA in a process referred to as error-prone translesion synthesis (TLS). TLS generates mutations targeted specifically to DNA ...
[45]
The Discovery of Error-prone DNA Polymerase V and Its Unique ...
Two proteins regulate the SOS response, LexA and RecA. LexA is a repressor that binds to more than 40 operators in the DNA damage-inducible regulon. Each ...<|separator|>
[46]
Spatial and temporal organization of RecA in the Escherichia coli ...
Feb 5, 2019 · The RecA protein orchestrates the cellular response to DNA damage via its multiple roles in the bacterial SOS response.
[47]
The SOS system: A complex and tightly regulated response to DNA ...
Efficient formation of RecA filaments in the extended conformation is necessary for SOS induction, even though ATP hydrolysis is not (Gruenig et al., 2009).
[48]
https://elifesciences.org/articles/42761
[49]
RecA Regulation by RecU and DprA During Bacillus subtilis Natural ...
We show that a null recA (ΔrecA) mutation suppresses the plasmid transformation defect of competent ΔrecU cells, and that RecU is essential for both chromosomal ...Missing: Neisseria | Show results with:Neisseria
[50]
https://www.cell.com/current-biology/fulltext/S0960-9822(16)31003-X
[51]
Direct involvement of DprA, the transformation-dedicated RecA ...
DprA has thus two key roles: ensuring production of transformants via interaction with RecA and competence shut-off via interaction with ComE, avoiding ...
[52]
Competence-specific induction of recA is required for full ... - PubMed
Competence-specific induction of recA is required for full recombination proficiency during transformation in Streptococcus pneumoniae.Missing: upregulation Neisseria
[53]
Natural transformation occurs independently of the essential actin ...
Nov 3, 2015 · In all transformable species recA is essential for transformation even when not part of the competence regulon, as for instance in Haemophilus ...<|control11|><|separator|>
[54]
The RecA-directed recombination pathway of natural transformation ...
RecA assembles dynamic filaments at those sites, as at DNA-damaged sites during their recombinational repair. Thus, RecA-directed tDNA homology search on the ...
[55]
Directed Evolution of RecA Variants with Enhanced Capacity ... - NIH
We use a kind of directed evolution to generate variants of the Escherichia coli RecA protein with an enhanced capacity to promote conjugational recombination.
[56]
Interactions between plasmids and other mobile genetic elements ...
Although co-integration can be catalyzed by host factors such as RecA and XerCD, it can also be mediated by mobile elements carried on plasmids.
[57]
RecA Inhibitors Potentiate Antibiotic Activity and Block Evolution of ...
They reduce the ability of bacteria to acquire antibiotic resistance mutations and to transfer mobile genetic elements conferring resistance. This study ...
[58]
what can be learnt from studying model conjugative plasmids ...
Jan 10, 2022 · Here, we review mechanisms employed by conjugative plasmids that promote their transmission and establishment in Gram-negative bacteria.During Conjugation · Ssdna Binding Proteins · After Conjugation
[59]
RAD51 Gene Family Structure and Function - PMC - PubMed Central
RAD51 is an ATPase that forms a nucleoprotein filament on single-stranded DNA. RAD51 has the function of finding and invading homologous DNA sequences to enable ...Missing: comparison | Show results with:comparison
[60]
RADX controls RAD51 filament dynamics to regulate replication fork ...
The RAD51 recombinase forms nucleoprotein filaments to promote double-strand break repair, replication fork reversal, and fork stabilization.
[61]
A novel Fanconi anaemia subtype associated with a dominant ...
Dec 18, 2015 · In line with this, mutant RAD51 acts as a dominant negative in an inducible cell model. In vitro, the mutation affected crucial steps in HR: ...
[62]
https://pmc.ncbi.nlm.nih.gov/articles/PMC7703940/
[63]
https://pmc.ncbi.nlm.nih.gov/articles/PMC7935748/
[64]
SOS response and its regulation on the fluoroquinolone resistance
A research has demonstrated that fluoroquinolone-resistance phenotype of a gyrA mutation was influenced by mutations in the recA gene, by the fact that recA142 ...
[65]
Enhanced antibiotic resistance development from fluoroquinolone ...
Mar 12, 2019 · ... mutant to more specifically probe the role of SOS induction. As ... Inhibition of mutation and combating the evolution of antibiotic resistance.
[66]
Quinolone Resistance Reversion by Targeting the SOS Response
Oct 10, 2017 · ... mutations in genes encoding the quinolone targets (DNA ... Inhibition of mutation and combating the evolution of antibiotic resistance.
[67]
Heteroresistance via beta-lactamase gene amplification threatens ...
Jun 7, 2022 · Heteroresistance (HR) is a form of resistance where a phenotypically unstable and often undetected minority resistant subpopulation co-exists ...Missing: RecA Pseudomonas aeruginosa
[68]
The DNA Damage Inducible SOS Response Is a Key ... - Frontiers
Aug 3, 2020 · The SOS response is an inducible DNA repair pathway controlled by two key regulators, LexA, a repressor, and RecA, an inducer.The SOS Response · Other Bacterial Stress... · The SOS Response and Biofilms
[69]
https://doi.org/10.1093/nar/13.20.7473
[70]
Antibiotic potentiators as a promising strategy for combating ... - Nature
Jun 6, 2025 · Moreover, 2-amino imidazole ... & Geyer, C. R. RecA inhibitors potentiate antibiotic activity and block evolution of antibiotic resistance.
[71]
An improved recombineering approach by adding RecA to lambda ...
Here we report that transient RecA co-expression enhances the total number of successful recombinations in bacterial artificial chromosomes (BACs), mostly ...Missing: editing | Show results with:editing
[72]
Redesign of ultrasensitive and robust RecA gene circuit to sense ...
Mar 4, 2021 · The redesigned P VRecA‐AT promoter showed a sensitive and robust response to DNA damage induced by UV and genotoxic compounds.
[73]
Recombination machinery engineering facilitates metabolic ... - NIH
Jul 1, 2021 · We here extensively engineered the recombination machinery by establishing a CRISPR-Cas9 based genome editing platform, which improved the homologous ...
[74]
Strategies to improve homology-based repair outcomes following ...
Jul 30, 2022 · This Cas9-RecA fusion construct increased SSA by 2.5-fold in HEK293T ... CRISPR-Cas9 fusion to dominant-negative 53BP1 enhances HDR and ...