RecA — Mediated Wiki

{{short description|DNA repair protein}} {{cs1 config|name-list-style=vanc|display-authors=6}} {{Infobox protein family | Symbol = RecA | Name = recA bacterial DNA recombination protein | image = RecA DNA 3CMT.png | width = | caption = Crystal structure of a RecA (rainbow colored)-DNA (magenta) complex. PDB ID: {{PDBe|3cmt}}.<ref>{{cite journal | vauthors = Chen Z, Yang H, Pavletich NP | date = May 2008 | title = Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures | journal = Nature | volume = 453 | issue = 7194 | pages = 489–484 | doi = 10.1038/nature06971 | pmid = 18497818 | bibcode = 2008Natur.453..489C | s2cid = 4416531 }}</ref> | Pfam = PF00154 | Pfam_clan = CL0023 | InterPro = IPR013765 | SMART = | PROSITE = PDOC00131 | MEROPS = | SCOP = 2reb | TCDB = | OPM family = | OPM protein = | CAZy = | CDD = }} {{Infobox nonhuman protein | Name = DNA recombination/repair protein RecA | image = | width = | caption = | Organism = ''Escherichia coli'' | TaxID = 83333 | Symbol = recA | AltSymbols = | EntrezGene = 947170 | HomoloGene = | PDB = 3CMT | RefSeqmRNA = | RefSeqProtein = NP_417179.1 | UniProt = P0A7G6 | ECnumber = 3.6.4.12 | Chromosome = Genomic | EntrezChromosome = NC_000913.3 | GenLoc_start = 2822708 | GenLoc_end = 2823769 }}

'''RecA''' is a 38 kilodalton protein essential for the repair and maintenance of DNA in bacteria.<ref>{{cite journal | vauthors = Horii T, Ogawa T, Ogawa H | date = January 1980 | title = Organization of the recA gene of Escherichia coli | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 77 | issue = 1 | pages = 313–317 | doi = 10.1073/pnas.77.1.313 | pmc = 348260 | pmid = 6244554 | bibcode = 1980PNAS...77..313H | doi-access = free }}</ref> It functions as a recombinase and strand-exchange protein, catalyzing the central steps of homologous recombination by forming nucleoprotein filaments on single-stranded DNA.<ref name="de Val2019" /> Structural and functional homologs to RecA have been found in all kingdoms of life.<ref>{{cite journal | vauthors = Lin Z, Kong H, Nei M, Ma H | date = July 2006 | title = Origins and evolution of the recA/RAD51 gene family: evidence for ancient gene duplication and endosymbiotic gene transfer | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 103 | issue = 27 | pages = 10328–10333 | doi = 10.1073/pnas.0604232103 | pmc = 1502457 | pmid = 16798872 | doi-access = free | bibcode = 2006PNAS..10310328L }}</ref><ref>{{cite journal | vauthors = Brendel V, Brocchieri L, Sandler SJ, Clark AJ, Karlin S | date = May 1997 | title = Evolutionary comparisons of RecA-like proteins across all major kingdoms of living organisms | journal = Journal of Molecular Evolution | volume = 44 | issue = 5 | pages = 528–541 | doi = 10.1007/pl00006177 | pmid = 9115177 | bibcode = 1997JMolE..44..528B }}</ref> RecA serves as an archetype for this class of homologous DNA repair proteins. The homologous protein is called RAD51 in eukaryotes and RadA in archaea.<ref>{{cite journal | vauthors = Shinohara A, Ogawa H, Ogawa T | date = May 1992 | title = Rad51 protein involved in repair and recombination in S. cerevisiae is a RecA-like protein | journal = Cell | volume = 69 | issue = 3 | pages = 457–470 | doi = 10.1016/0092-8674(92)90447-k | pmid = 1581961 | bibcode = 1992Cell...69..457S | s2cid = 35937283 }}</ref><ref>{{cite journal | vauthors = Seitz EM, Brockman JP, Sandler SJ, Clark AJ, Kowalczykowski SC | date = May 1998 | title = RadA protein is an archaeal RecA protein homolog that catalyzes DNA strand exchange | journal = Genes & Development | volume = 12 | issue = 9 | pages = 1248–1253 | doi = 10.1101/gad.12.9.1248 | pmc = 316774 | pmid = 9573041 }}</ref>

RecA has multiple activities, all related to DNA repair. As a recombinase, it mediates ATP-dependent strand exchange between homologous DNA molecules, driving the key pairing and heteroduplex formation steps of recombinational repair.<ref name="de Val2019" /> In the bacterial SOS response, it functions as a co-protease<ref>{{cite journal | vauthors = Horii T, Ogawa T, Nakatani T, Hase T, Matsubara H, Ogawa H | date = December 1981 | title = Regulation of SOS functions: purification of E. coli LexA protein and determination of its specific site cleaved by the RecA protein | journal = Cell | volume = 27 | issue = 3 Pt 2 | pages = 515–522 | doi = 10.1016/0092-8674(81)90393-7 | pmid = 6101204 | s2cid = 45482725 }}</ref> in the autocatalytic cleavage of the LexA repressor and the λ repressor.<ref>{{cite journal | vauthors = Little JW | date = March 1984 | title = Autodigestion of lexA and phage lambda repressors | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 81 | issue = 5 | pages = 1375–1379 | doi = 10.1073/pnas.81.5.1375 | pmc = 344836 | pmid = 6231641 | bibcode = 1984PNAS...81.1375L | doi-access = free }}</ref>

== Structure ==

The ''E. coli'' RecA monomer (352 amino acids, ~37.8 kDa) is organized into three structural domains: * small N-terminal domain (NTD, residues ~1–33) The NTD mediates monomer–monomer interactions during filament polymerization and additionally facilitates presynaptic filament formation and dsDNA capture, functions that are evolutionarily conserved across the RecA/RAD51/RadA family.<ref name="Bell_2016" /> * central core ATPase domain (CAD, residues ~34–240) The CAD constitutes the functional heart of the protein, housing two Walker motifs (Walker A (P-loop) and Walker B) responsible for ATP binding and hydrolysis, as well as the DNA-binding loops L1 and L2 that contact single-stranded DNA within the filament.<ref name="de Val2019" /> * large C-terminal domain (CTD, residues ~241–352).<ref name="Bell_2016">{{cite journal | vauthors = Bell JC, Kowalczykowski SC | date = July 2016 | title = RecA: Regulation and Mechanism of a Molecular Search Engine | journal = Trends in Biochemical Sciences | volume = 41 | issue = 7 | pages = 491–507 | doi = 10.1016/j.tibs.2016.04.002 | pmc = 4892382 | pmid = 27156412 }}</ref> The CTD contributes to secondary DNA binding (the interaction with the incoming duplex during homology search) and contains a second nucleotide-binding site implicated in allosteric regulation of filament activity.<ref name="Chandran_2012">{{cite journal | vauthors = Chandran A, Vijayan M | date = October 2012 | title = Allosteric movements in eubacterial RecA | journal = Biophysical Reviews | volume = 4 | issue = 3 | pages = 199–208 | doi = 10.1007/s12551-012-0097-4 | pmc = 5418409 | pmid = 28510010 }}</ref>

RecA monomers polymerize cooperatively onto ssDNA in the presence of ATP to form a right-handed helical nucleoprotein filament with approximately 6 monomers per turn and a helical pitch of ~95 Å, in which the DNA is stretched ~1.5-fold relative to B-form and held in a conformation competent for homology search and strand exchange.<ref name="de Val2019" /><ref name="Bell_2016" /> The filament exists in two conformational states — an extended, ATP-bound active form and a compressed, ADP-bound inactive form — with cooperative transitions between neighboring monomers ensuring that the filament remains catalytically competent throughout the ATPase cycle.<ref name="Chandran_2012" /><ref name="Bell_2016" />

== Function == === Homologous recombination === The RecA protein binds strongly and in long clusters to ssDNA to form a nucleoprotein filament.<ref name="RecASynapse">{{cite book | vauthors = Henkin TM, Peters JE, Snyder L, Champness W | date = 2020 | title = Snyder & Champness molecular genetics of bacteria | publisher = Wiley | edition = Fifth | pages = 368–371 | isbn = 978-1-55581-975-0 | location = Hoboken, NJ }}</ref> This is also called a presynaptic filament.<ref name="de Val2019" /> The presynaptic filament has an inactive and active conformation. RecA must be bound to ATP to form an active filament. The activated filament searches for a homologous region of dsDNA to bind to, a process known as synapsis.

The mechanisms of the RecA homology search are not fully understood.<ref name="RecASynapse" /><ref name="Hu2024">{{cite journal | vauthors = Hu J, Crickard JB | date = February 2024 | title = All who wander are not lost: the search for homology during homologous recombination | journal = Biochemical Society Transactions | volume = 52 | issue = 1 | pages = 367–377 | doi = 10.1042/BST20230705 | pmc = 10903458 | pmid = 38323621 }}</ref> The RecA filament searches the dsDNA in 8 base pair segments.<ref name=Wright2018>{{cite journal | vauthors = Wright WD, Shah SS, Heyer WD | date = July 2018 | title = Homologous recombination and the repair of DNA double-strand breaks | journal = The Journal of Biological Chemistry | volume = 293 | issue = 27 | pages = 10524–10535 | doi = 10.1074/jbc.TM118.000372 | pmc = 6036207 | pmid = 29599286 | doi-access = free }}</ref> When the threshold of 8-bases of homology is exceeded, the filament complex is stabilized.<ref name="de Val2019">{{cite journal | vauthors = Del Val E, Nasser W, Abaibou H, Reverchon S | date = October 2019 | title = RecA and DNA recombination: a review of molecular mechanisms | journal = Biochemical Society Transactions | volume = 47 | issue = 5 | pages = 1511–1531 | doi = 10.1042/BST20190558 | pmid = 31654073 | url = https://hal.science/hal-02320683 }}</ref> In 2021, Witkor et al., demonstrated that the RecA filament uses a "reduced dimensionality" search mechanism.<ref>{{cite journal | vauthors = Wiktor J, Gynnå AH, Leroy P, Larsson J, Coceano G, Testa I, Elf J | date = September 2021 | title = RecA finds homologous DNA by reduced dimensionality search | journal = Nature | volume = 597 | issue = 7876 | pages = 426–429 | doi = 10.1038/s41586-021-03877-6 | pmc = 8443446 | pmid = 34471288 | bibcode = 2021Natur.597..426W }}</ref><ref>{{cite journal | vauthors = Lalande E, El Sayyed H | date = February 2022 | title = Break-ups and make-ups: DNA search and repair | journal = Nature Reviews. Microbiology | volume = 20 | issue = 2 | pages = 66 | doi = 10.1038/s41579-021-00671-z | pmid = 34873308 }}</ref>

Once the filament has located and bound to a complementary sequence of dsDNA, strand exchange occurs.<ref name="RecASynapse" /> This reaction occurs in the 5' to 3' direction.<ref name="Hu2024" />

Since it is a DNA-dependent ATPase, RecA contains an additional site for binding and hydrolyzing ATP. RecA associates more tightly with DNA when it has ATP bound than when it has ADP bound.<ref>{{cite journal | vauthors = Reitz D, Chan YL, Bishop DK | date = December 2021 | title = How strand exchange protein function benefits from ATP hydrolysis | journal = Current Opinion in Genetics & Development | volume = 71 | pages = 120–128 | doi = 10.1016/j.gde.2021.06.016 | pmc = 8671154 | pmid = 34343922 }}</ref>

Homologous recombination events mediated by RecA can occur in ''Escherichia coli'' during the period after DNA replication when sister loci remain close. RecA can also mediate homology pairing, homologous recombination, and DNA break repair between distant sister loci that had segregated to opposite halves of the ''E. coli'' cell.<ref name="Lesterlin2014">{{cite journal | vauthors = Lesterlin C, Ball G, Schermelleh L, Sherratt DJ | date = February 2014 | title = RecA bundles mediate homology pairing between distant sisters during DNA break repair | journal = Nature | volume = 506 | issue = 7487 | pages = 249–253 | doi = 10.1038/nature12868 | pmc = 3925069 | pmid = 24362571 | bibcode = 2014Natur.506..249L }}</ref>

===Natural transformation=== {{main|Natural competence}} Natural bacterial transformation involves the transfer of DNA from one bacterium to another (ordinarily of the same species) and the integration of the donor DNA into the recipient chromosome by homologous recombination, a process mediated by the RecA protein. In some bacteria, the ''recA'' gene is induced in response to the bacterium becoming competent, the physiological state required for transformation.<ref name="RecACompetence">{{cite book | vauthors = Henkin TM, Peters JE, Snyder L, Champness W | date = 2020 | title = Snyder & Champness molecular genetics of bacteria | publisher = Wiley | edition = Fifth | page = 259 | isbn = 978-1-55581-975-0 | location = Hoboken, NJ }}</ref>

==Clinical significance== RecA has been proposed as a potential drug target for bacterial infections.<ref name="Culyba2015">{{cite journal | vauthors = Culyba MJ, Mo CY, Kohli RM | date = June 2015 | title = Targets for Combating the Evolution of Acquired Antibiotic Resistance | journal = Biochemistry | volume = 54 | issue = 23 | pages = 3573–3582 | doi = 10.1021/acs.biochem.5b00109 | pmc = 4471857 | pmid = 26016604 }}</ref> Small molecules that interfere with RecA function have been identified.<ref name="Merrikh2020">{{cite journal | vauthors = Merrikh H, Kohli RM | date = October 2020 | title = Targeting evolution to inhibit antibiotic resistance | journal = The FEBS Journal | volume = 287 | issue = 20 | pages = 4341–4353 | doi = 10.1111/febs.15370 | pmc = 7578009 | pmid = 32434280 }}</ref><ref>{{cite journal | vauthors = Wigle TJ, Singleton SF | date = June 2007 | title = Directed molecular screening for RecA ATPase inhibitors | journal = Bioorganic & Medicinal Chemistry Letters | volume = 17 | issue = 12 | pages = 3249–3253 | doi = 10.1016/j.bmcl.2007.04.013 | pmc = 1933586 | pmid = 17499507 }}</ref> Since many antibiotics lead to DNA damage, and all bacteria rely on RecA to fix this damage, inhibitors of RecA could be used to enhance the toxicity of antibiotics. Inhibitors of RecA may also delay or prevent the appearance of bacterial drug resistance.<ref name="Culyba2015" />

==History== RecA was discovered in 1965 by Alvin J. Clark and Ann Dee Margulies in genetic screens for recombination deficient strains of ''E. coli''.<ref name="Bell2016">{{cite journal | vauthors = Bell JC, Kowalczykowski SC | date = June 2016 | title = RecA: Regulation and Mechanism of a Molecular Search Engine | journal = Trends in Biochemical Sciences | volume = 41 | issue = 6 | pages = 491–507 | doi = 10.1016/j.tibs.2016.04.002 | pmc = 4892382 | pmid = 27156117 }}</ref><ref>{{cite journal | vauthors = Clark AJ, Margulies AD | date = February 1965 | title = Isolation and characterization of recombination-deficient mutants of ''Escherichia coli'' K12 | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 53 | issue = 2 | pages = 451–459 | doi = 10.1073/pnas.53.2.451 | pmc = 219534 | pmid = 14294081 | doi-access = free | bibcode = 1965PNAS...53..451C }}</ref> The gene name "rec", first published in 1969, was chosen to indicate its involvement in recombination.<ref name="Clark1996">{{cite journal | vauthors = Clark AJ | date = September 1996 | title = recA mutants of E. coli K12: a personal turning point | journal = BioEssays | volume = 18 | issue = 9 | pages = 767–772 | doi = 10.1002/bies.950180912 | pmid = 8831293 }}</ref><ref>{{cite journal | vauthors = Clark AJ | date = October 1967 | title = The beginning of a genetic analysis of recombination proficiency | journal = Journal of Cellular Physiology | volume = 70 | issue = 2 | article-number = Suppl:165–80 | doi = 10.1002/jcp.1040700412 | pmid = 4867583 }}</ref><ref>{{cite journal | vauthors = Redfield RJ | date = August 2001 | title = Do bacteria have sex? | journal = Nature Reviews. Genetics | volume = 2 | issue = 8 | pages = 634–639 | doi = 10.1038/35084593 | pmid = 11483988 }}</ref> In 1976, the ''recA'' gene was cloned for the first time by Kevin McEntee.<ref>{{cite journal | vauthors = Roca AI, Cox MM | date = January 1990 | title = The RecA protein: structure and function | journal = Critical Reviews in Biochemistry and Molecular Biology | volume = 25 | issue = 6 | pages = 415–456 | doi = 10.3109/10409239009090617 | pmid = 2292186 }}</ref><ref>{{cite journal | vauthors = McEntee K | date = March 1976 | title = Specialized transduction of recA by bacteriophage lambda | journal = Virology | volume = 70 | issue = 1 | pages = 221–222 | doi = 10.1016/0042-6822(76)90258-0 | pmid = 769310 }}</ref> Shortly after, the protein was purified for the first time by several groups.<ref name="Clark1996" /><ref name="Bell2016"/> Purification of the protein led to a number of breakthroughs on the biochemical properties of RecA. The first crystal structure of RecA was published in 1992, nearly 30 years after the protein was discovered.<ref>{{cite journal | vauthors = Story RM, Weber IT, Steitz TA | date = January 1992 | title = The structure of the E. coli recA protein monomer and polymer | journal = Nature | volume = 355 | issue = 6358 | pages = 318–325 | doi = 10.1038/355318a0 | pmid = 1731246 | bibcode = 1992Natur.355..318S }}</ref>

Later research identified related proteins, including RecBCD and RecF.<ref name="Bell2016" /><ref>{{cite journal | vauthors = Cox MM | date = July 2001 | title = Historical overview: searching for replication help in all of the rec places | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 98 | issue = 15 | pages = 8173–8180 | doi = 10.1073/pnas.131004998 | pmc = 37418 | pmid = 11459950 | doi-access = free | bibcode = 2001PNAS...98.8173C }}</ref>

== References == {{Reflist}}

Category:Bacterial proteins Category:DNA repair