RecA Protein


The RecA protein of Escherichia coli is the prototypic deoxyribonucleic acid (DNA)‐strand exchange protein. It assembles on single‐stranded DNA to form a helical nucleoprotein filament that is the active species for all RecA protein‐dependent functions. This protein–DNA complex is responsible for three mutually exclusive functions: DNA recombination, induction of the DNA‐damage SOS response and SOS‐induced mutagenesis. The overall structure and activity of the nucleoprotein filament are determined by nucleoside triphosphate (NTP) cofactor binding, hydrolysis and product release. This is evident when the crystal structure of the filament is closely examined and NTP‐related structural changes are related to biological function.

Key Concepts

  • RecA protein is the prototype enzyme for a family of proteins known as recombinases.
  • Homologous recombination is the exchange of the corresponding stretches of DNA between two DNA molecules of similar sequence.
  • The SOS response is an inducible DNA repair and damage tolerance system that is induced by RecA.
  • SOS‐induced mutagenesis is a form of DNA repair catalysed by error‐prone, translesion DNA polymerases.
  • The RecA nucleoprotein filament is a large dynamic structure whose formation is essential to all RecA functions.
  • Coprotease activity is the induced self‐cleavage of one protein (LexA) by another (RecA).

Keywords: DNA‐strand exchange; genetic recombination; SOS response; SOS mutagenesis; nucleoprotein filament; LexA repressor

Figure 1. Roles of the RecA nucleoprotein filament in DNA metabolism. A schematic showing the three mutually exclusive functions of the RecA protein filament. The LexA–DNA complex is from Zhang et al. and the docked RecA–LexA complex is taken from Butala et al. . M. Butala (University of Ljubljana, Slovenia) provided the coordinates for the docked complex. The structure of the RecA nucleoprotein filament and the three‐strand product complex in homologous recombination are adapted from Chen et al. . Coordinates for the UmuC model were provided by M. Goodman (University of Southern California, USA) and were published in Gruber et al. and those of UmuD′ are from Peat et al. . Structures were artistically docked to create Pol V and the mutasomes.
Figure 2. ATP binding converts RecA from the inactive to the active state. (a) A single turn of the filament is shown in schematic form. Inset: the location of the ATP binding site at the monomer–monomer interface. The 5′‐proximal RecA is coloured in cyan, with the Walker A and B residues coloured yellow and pale pink, respectively. K72, which is the key residue in the Walker A box, is highlighted in green for clarity. When this reside us mutated, ATPase activity is essentially abolished. Red, ATP. The 3′‐distal monomer is coloured orange and key lysine residues from this subunit involved in ATPase activity are coloured purple. Coordinates for this image are from Chen et al. . (b,c) Three‐dimensional reconstructions of electron micrographs of RecA filaments formed on dsDNA with ADP (b) or ATPγS (c) (VanLoock et al., ). (d,e) Single turns of the RecA filament as seen in the crystal structure (Chen et al., ), (d) Inactive and (e) active filaments. In the absence of ATP or in the presence of ADP, the RecA filament is in a collapsed or inactive state (left side of a, and panels b and d). Once ATP binds, the filament becomes active (the right side of a and panels c and e).
Figure 3. The structure of the pre‐ and postsynaptic RecA filament. (a) A single turn of the presynaptic RecA filament. RecA monomers are coloured green, cyan and brown; ssDNA is in red and the location of ATP is indicated by the fuchsia Connolly surfaces. (b) The postsynaptic filament with the product complex located approximately in the centre. The incoming strand of DNA is coloured blue. Black lines, filament axis. (c and d) The DNA within the pre‐ and postsynaptic complexes is shown with dsDNA for comparison. In the schematic, the phosphodiester backbones are coloured light green and pale orange, so that the perpendicular arrangement of the bases (coloured purple and blue) is evident. Coordinates for this image were taken from Chen et al. .
Figure 4. The structure of the nucleoprotein filament is conserved. Electron micrographs of nucleoprotein filaments formed on dsDNA. (a) RecA nucleoprotein filament assembled on nicked, circular dsDNA. (b) UvsX nucleoprotein filament assembled on linear M13 dsDNA. (c) Rad51 nucleoprotein filament assembled on nicked, circular ϕX dsDNA. The scale bar in panels (a) and (b) are 0.1 µm. In panel (c), the tobacco mosaic virus particles (indicated by the arrows) are approximately 200 nm in diameter. A more comprehensive version of this figure and legend appears in Bianco et al. .
Figure 5. The DNA‐strand exchange reaction promoted by the RecA protein. RecA is represented as blue spheres and ssDNA‐binding (SSB) protein as orange squares. ssDNA is black and dsDNA is coloured green. The three stages shown are presynapsis (a), synapsis (b) and DNA heteroduplex extension or branch migration (c). Adapted from Tan et al. 2017 © John Wiley and Sons Ltd.


Bell JC, Plank JL, Dombrowski CC and Kowalczykowski SC (2012) Direct imaging of RecA nucleation and growth on single molecules of SSB‐coated ssDNA. Nature 491 (7423): 274–278.

Bell JC, Liu B and Kowalczykowski SC (2015) Imaging and energetics of single SSB‐ssDNA molecules reveal intramolecular condensation and insight into RecOR function. eLife 4: e08646.

Bianco PR, Tracy RB and Kowalczykowski SC (1998) DNA strand exchange proteins: a biochemical and physical comparison. Frontiers in Bioscience 3: D570–D603.

Butala M, Klose D, Hodnik V, et al. (2011) Interconversion between bound and free conformations of LexA orchestrates the bacterial SOS response. Nucleic Acids Research 39 (15): 6546–6557.

Chen Z, Yang H and Pavletich NP (2008) Mechanism of homologous recombination from the RecA‐ssDNA/dsDNA structures. Nature 453 (7194): 489–494.

Courcelle J, Khodursky A, Peter B, Brown PO and Hanawalt PC (2001) Comparative gene expression profiles following UV exposure in wild‐type and SOS‐deficient Escherichia coli. Genetics 158 (1): 41–64.

Cox MM and Lehman IR (1981) recA protein of Escherichia coli promotes branch migration, a kinetically distinct phase of DNA strand exchange. Proceedings of the National Academy of Sciences of the United States of America 78 (6): 3433–3437.

De Vlaminck I, van Loenhout MT, Zweifel L, et al. (2012) Mechanism of homology recognition in DNA recombination from dual‐molecule experiments. Molecular Cell 46 (5): 616–624.

Dillingham MS and Kowalczykowski SC (2008) RecBCD enzyme and the repair of double‐stranded DNA breaks. Microbiology and Molecular Biology Reviews 72: 642–671.

Fagerburg MV, Schauer GD, Thickman KR, et al. (2012) PcrA‐mediated disruption of RecA nucleoprotein filaments – essential role of the ATPase activity of RecA. Nucleic Acids Research 40 (17): 8416–8424.

Goodman MF (2014) The discovery of error‐prone DNA polymerase V and its unique regulation by RecA and ATP. Journal of Biological Chemistry 289 (39): 26772–26782.

Gruber AJ, Erdem AL, Sabat G, et al. (2015) A RecA protein surface required for activation of DNA polymerase V. PLoS Genetics 11 (3): e1005066.

Gupta S, Yeeles JT and Marians KJ (2014) Regression of replication forks stalled by leading‐strand template damage: II. Regression by RecA is inhibited by SSB. Journal of Biological Chemistry 289 (41): 28388–28398.

Handa N, Morimatsu K, Lovett ST and Kowalczykowski SC (2009) Reconstitution of initial steps of dsDNA break repair by the RecF pathway of E. coli. Genes & Development 23 (10): 1234–1245.

Howard‐Flanders P, West SC and Stasiak A (1984) Role of RecA protein spiral filaments in genetic recombination. Nature (London) 309 (5965): 215–219.

Indiani C, Patel M, Goodman MF and O'Donnell ME (2013) RecA acts as a switch to regulate polymerase occupancy in a moving replication fork. Proceedings of the National Academy of Sciences of the United States of America 110 (14): 5410–5415.

Kim JI and Cox MM (2002) The RecA proteins of Deinococcus radiodurans and Escherichia coli promote DNA strand exchange via inverse pathways. Proceedings of the National Academy of Sciences of the United States of America 99 (12): 7917–7921.

Kogoma T (1996) Recombination by replication. Cell 85 (5): 625–627.

Kowalczykowski SC and Krupp RA (1995) DNA‐strand exchange promoted by RecA protein in the absence of ATP: implications for the mechanism of energy transduction in protein‐promoted nucleic acid transactions. Proceedings of the National Academy of Sciences of the United States of America 92 (8): 3478–3482.

Mazin AV and Kowalczykowski SC (1996) The specificity of the secondary DNA binding site of RecA protein defines its role in DNA strand exchange. Proceedings of the National Academy of Sciences of the United States of America 93 (20): 10673–10678.

Mazin AV and Kowalczykowski SC (1998) The function of the secondary DNA‐binding site of RecA protein during DNA strand exchange. EMBO Journal 17 (4): 1161–1168.

Menetski JP, Bear DG and Kowalczykowski SC (1990) Stable DNA heteroduplex formation catalyzed by the Escherichia coli RecA protein in the absence of ATP hydrolysis. Proceedings of the National Academy of Sciences of the United States of America 87: 21–25.

Morimatsu K and Kowalczykowski SC (2003) RecFOR proteins load RecA protein onto gapped DNA to accelerate DNA strand exchange: a universal step of recombinational repair. Molecular Cell 11 (5): 1337–1347.

Morimatsu K, Wu Y and Kowalczykowski SC (2012) RecFOR proteins target RecA protein to a DNA gap with either DNA or RNA at the 5′ terminus: implication for repair of stalled replication forks. Journal of Biological Chemistry 287 (42): 35621–35630.

Nohmi T, Battista JR, Dodson LA and Walker GC (1988) RecA‐mediated cleavage activates UmuD for mutagenesis: mechanistic relationship between transcriptional derepression and posttranslational activation. Proceedings of the National Academy of Sciences of the United States of America 85: 1816–1820.

Ogawa T, Wabiko H, Tsurimoto T, et al. (1978) Characteristics of purified recA protein and the regulation of its synthesis in vivo. Cold Spring Harbor Symposia on Quantitative Biology 43: 909–916.

Ogawa T, Yu X, Shinohara A and Egelman EH (1993) Similarity of the yeast RAD51 filament to the bacterial RecA filament. Science 259 (5103): 1896–1899.

Peat TS, Frank EG, McDonald JP, et al. (1996) Structure of the UmuD' protein and its regulation in response to DNA damage. Nature 380 (6576): 727–730.

Petrova V, Chen SH, Molzberger ET, et al. (2015) Active displacement of RecA filaments by UvrD translocase activity. Nucleic Acids Research 43 (8): 4133–4149.

Qi Z, Redding S, Lee JY, et al. (2015) DNA sequence alignment by microhomology sampling during homologous recombination. Cell 160 (5): 856–869.

Register JC III and Griffith J (1985) The direction of RecA protein assembly onto single strand DNA is the same as the direction of strand assimilation during strand exchange. Journal of Biological Chemistry 260: 12308–12312.

Roberts JW, Roberts CW, Craig NL and Phizicky EM (1978) Activity of the Escherichia coli recA‐gene product. Cold Spring Harbor Symposia on Quantitative Biology 43: 917–920.

Shibata T, DasGupta C, Cunningham RP and Radding CM (1979) Purified Escherichia coli recA protein catalyzes homologous pairing of superhelical DNA and single‐stranded fragments. Proceedings of the National Academy of Sciences of the United States of America 76: 1638–1642.

Tan HY, Wilczek LA, Pottinger S, et al. (2017) The intrinsically disordered linker of E. coli SSB is critical for the release from single‐stranded DNA. Protein Science 26 (4): 700–717.

Tang M, Shen X, Frank EG, et al. (1999) UmuD′(2)C is an error‐prone DNA polymerase, Escherichia coli pol V. Proceedings of the National Academy of Sciences of the United States of America 96 (16): 8919–8924.

Taniguchi Y, Choi PJ, Li GW, et al. (2010) Quantifying E. coli proteome and transcriptome with single‐molecule sensitivity in single cells. Science 329 (5991): 533–538.

Umezu K, Chi NW and Kolodner RD (1993) Biochemical interaction of the Escherichia coli RecF, RecO, and RecR proteins with RecA protein and single‐stranded DNA binding protein. Proceedings of the National Academy of Sciences of the United States of America 90 (9): 3875–3879.

VanLoock MS, Yu X, Yang S, et al. (2003) ATP‐mediated conformational changes in the RecA filament. Structure 11 (2): 187–196.

Weinstock GM, McEntee K and Lehman IR (1981a) Hydrolysis of nucleoside triphosphates catalyzed by the recA protein of Escherichia coli. Characterization of ATP hydrolysis. Journal of Biological Chemistry 256 (16): 8829–8834.

Weinstock GM, McEntee K and Lehman IR (1981b) Hydrolysis of nucleoside triphosphates catalyzed by the recA protein of Escherichia coli. Hydrolysis of UTP. Journal of Biological Chemistry 256 (16): 8856–8858.

Yang S, Yu X, Seitz EM, Kowalczykowski SC and Egelman EH (2001) Archaeal RadA protein binds DNA as both helical filaments and octameric rings. Journal of Molecular Biology 314 (5): 1077–1085.

Zaitsev EN and Kowalczykowski SC (2000) A novel pairing process promoted by Escherichia coli RecA protein: inverse DNA and RNA strand exchange. Genes & Development 14 (6): 740–749.

Zhang AP, Pigli YZ and Rice PA (2010) Structure of the LexA‐DNA complex and implications for SOS box measurement. Nature 466 (7308): 883–886.

Further Reading

Bell JC and Kowalczykowski SC (2016a) Mechanics and single‐molecule interrogation of DNA recombination. Annual Review of Biochemistry 85: 193–226.

Bell JC and Kowalczykowski SC (2016b) RecA: regulation and mechanism of a molecular search engine (Trends in Biochemical Sciences, June 2016, Vol. 41, No. 6, 491–507). Trends in Biochemical Sciences 41 (7): 646.

Bianco PR (2010) DNA helicases. EcoSal Plus 4 (1): 1–23.

Cox MM (2007) Regulation of bacterial RecA protein function. Critical Reviews in Biochemistry and Molecular Biology 42 (1): 41–63.

Goodman MF and Woodgate R (2013) Translesion DNA polymerases. Cold Spring Harbor Perspectives in Biology 5 (10): a010363.

Goodman MF, McDonald JP, Jaszczur MM and Woodgate R (2016) Insights into the complex levels of regulation imposed on Escherichia coli DNA polymerase V. DNA Repair (Amst) 44: 42–50.

Kelley WL (2006) Lex marks the spot: the virulent side of SOS and a closer look at the LexA regulon. Molecular Microbiology 62 (5): 1228–1238.

Michel B and Leach D (2012) Homologous recombination‐enzymes and pathways. EcoSal Plus 5 (1): 1–46.

Simmons LA, Foti JJ, Cohen SE and Walker GC (2008) The SOS regulatory network. EcoSal Plus 3 (1): 1–30.

Stasiak A and Di Capua E (1982) The helicity of DNA in complexes with RecA protein. Nature 299: 185–186.

Vaisman A, McDonald JP and Woodgate R (2012) Translesion DNA synthesis. EcoSal Plus 5 (1): 1–32.

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Bianco, Piero R(Mar 2018) RecA Protein. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0000584.pub3]