RecA

Last updated
recA bacterial DNA recombination protein
Homologous recombination 3cmt.png
Crystal structure of a RecA-DNA complex. PDB ID: 3cmt . [1]
Identifiers
SymbolRecA
Pfam PF00154
Pfam clan CL0023
InterPro IPR013765
PROSITE PDOC00131
SCOP2 2reb / SCOPe / SUPFAM
Available protein structures:
Pfam   structures / ECOD  
PDB RCSB PDB; PDBe; PDBj
PDBsum structure summary

RecA is a 38 kilodalton protein essential for the repair and maintenance of DNA in bacteria. [2] Structural and functional homologs to RecA have been found in all kingdoms of life. [3] [4] 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. [5] [6]

Contents

RecA has multiple activities, all related to DNA repair. In the bacterial SOS response, it has a co-protease [7] function in the autocatalytic cleavage of the LexA repressor and the λ repressor. [8]

Function

Homologous recombination

The RecA protein binds strongly and in long clusters to ssDNA to form a nucleoprotein filament. [9] The protein has more than one DNA binding site, and thus can hold a single strand and double strand together. This feature makes it possible to catalyze a DNA synapsis reaction between a DNA double helix and a complementary region of single-stranded DNA. The RecA-ssDNA filament searches for sequence similarity along the dsDNA. A disordered DNA loop in RecA, Loop 2, contains the residues responsible for DNA homologous recombination. [10] In some bacteria, RecA posttranslational modification via phosphorylation of a serine residue on Loop 2 can interfere with homologous recombination. [11]

There are multiple proposed models for how RecA finds complementary DNA. [9] In one model, termed conformational proofreading, the DNA duplex is stretched, which enhances sequence complementarity recognition. [12] [13] The reaction initiates the exchange of strands between two recombining DNA double helices. After the synapsis event, in the heteroduplex region a process called branch migration begins. In branch migration an unpaired region of one of the single strands displaces a paired region of the other single strand, moving the branch point without changing the total number of base pairs. Spontaneous branch migration can occur, however, as it generally proceeds equally in both directions it is unlikely to complete recombination efficiently. The RecA protein catalyzes unidirectional branch migration and by doing so makes it possible to complete recombination, producing a region of heteroduplex DNA that is thousands of base pairs long.

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. [14]

In Escherichia coli , homologous recombination events mediated by RecA can occur 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. [15]

Natural transformation

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. [16] In Bacillus subtilis the length of the transferred DNA can be as great as a third and up to the size of the whole chromosome. [17] [18]

Clinical significance

RecA has been proposed as a potential drug target for bacterial infections. [19] Small molecules that interfere with RecA function have been identified. [20] [21] 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. [19]

Related Research Articles

<span class="mw-page-title-main">Chromosomal crossover</span> Cellular process

Chromosomal crossover, or crossing over, is the exchange of genetic material during sexual reproduction between two homologous chromosomes' non-sister chromatids that results in recombinant chromosomes. It is one of the final phases of genetic recombination, which occurs in the pachytene stage of prophase I of meiosis during a process called synapsis. Synapsis begins before the synaptonemal complex develops and is not completed until near the end of prophase I. Crossover usually occurs when matching regions on matching chromosomes break and then reconnect to the other chromosome.

<span class="mw-page-title-main">Genetic recombination</span> Production of offspring with combinations of traits that differ from those found in either parent

Genetic recombination is the exchange of genetic material between different organisms which leads to production of offspring with combinations of traits that differ from those found in either parent. In eukaryotes, genetic recombination during meiosis can lead to a novel set of genetic information that can be further passed on from parents to offspring. Most recombination occurs naturally and can be classified into two types: (1) interchromosomal recombination, occurring through independent assortment of alleles whose loci are on different but homologous chromosomes ; & (2) intrachromosomal recombination, occurring through crossing over.

<span class="mw-page-title-main">SOS response</span> Cell response to DNA damage

The SOS response is a global response to DNA damage in which the cell cycle is arrested and DNA repair and mutagenesis are induced. The system involves the RecA protein. The RecA protein, stimulated by single-stranded DNA, is involved in the inactivation of the repressor (LexA) of SOS response genes thereby inducing the response. It is an error-prone repair system that contributes significantly to DNA changes observed in a wide range of species.

<span class="mw-page-title-main">RecBCD</span> Family of protein complexes in bacteria

Exodeoxyribonuclease V is an enzyme of E. coli that initiates recombinational repair from potentially lethal double strand breaks in DNA which may result from ionizing radiation, replication errors, endonucleases, oxidative damage, and a host of other factors. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. It catalyses exonucleolytic cleavage in either 5′- to 3′- or 3′- to 5′-direction to yield 5′-phosphooligonucleotides.

RecQ helicase is a family of helicase enzymes initially found in Escherichia coli that has been shown to be important in genome maintenance. They function through catalyzing the reaction ATP + H2O → ADP + P and thus driving the unwinding of paired DNA and translocating in the 3' to 5' direction. These enzymes can also drive the reaction NTP + H2O → NDP + P to drive the unwinding of either DNA or RNA.

<span class="mw-page-title-main">Non-homologous end joining</span> Pathway that repairs double-strand breaks in DNA

Non-homologous end joining (NHEJ) is a pathway that repairs double-strand breaks in DNA. It is called "non-homologous" because the break ends are directly ligated without the need for a homologous template, in contrast to homology directed repair (HDR), which requires a homologous sequence to guide repair. NHEJ is active in both non-dividing and proliferating cells, while HDR is not readily accessible in non-dividing cells. The term "non-homologous end joining" was coined in 1996 by Moore and Haber.

<i>Mycobacterium smegmatis</i> Species of bacterium

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<span class="mw-page-title-main">Homologous recombination</span> Genetic recombination between identical or highly similar strands of genetic material

Homologous recombination is a type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids.

Recombineering is a genetic and molecular biology technique based on homologous recombination systems, as opposed to the older/more common method of using restriction enzymes and ligases to combine DNA sequences in a specified order. Recombineering is widely used for bacterial genetics, in the generation of target vectors for making a conditional mouse knockout, and for modifying DNA of any source often contained on a bacterial artificial chromosome (BAC), among other applications.

Recombinases are genetic recombination enzymes.

<span class="mw-page-title-main">RAD51</span> Protein involved in DNA repair

DNA repair protein RAD51 homolog 1 is a protein encoded by the gene RAD51. The enzyme encoded by this gene is a member of the RAD51 protein family which assists in repair of DNA double strand breaks. RAD51 family members are homologous to the bacterial RecA, Archaeal RadA, and yeast Rad51. The protein is highly conserved in most eukaryotes, from yeast to humans.

<span class="mw-page-title-main">RAD52</span> Protein-coding gene in the species Homo sapiens

RAD52 homolog , also known as RAD52, is a protein which in humans is encoded by the RAD52 gene.

<span class="mw-page-title-main">XRCC2</span> Protein-coding gene in the species Homo sapiens

DNA repair protein XRCC2 is a protein that in humans is encoded by the XRCC2 gene.

<span class="mw-page-title-main">DMC1 (gene)</span> Protein-coding gene in the species Homo sapiens

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Conformational proofreading or conformational selection is a general mechanism of molecular recognition systems, suggested by Yonatan Savir and Tsvi Tlusty, in which introducing an energetic barrier - such as a structural mismatch between a molecular recognizer and its target - enhances the recognition specificity and quality. Conformational proofreading does not require the consumption of energy and may therefore be used in any molecular recognition system. Conformational proofreading is especially useful in scenarios where the recognizer has to select the appropriate target among many similar competitors. Proteins evolve the capacity for conformational proofreading through fine-tuning their geometry, flexibility and chemical interactions with the target.

<span class="mw-page-title-main">Synthesis-dependent strand annealing</span>

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Bacterial recombination is a type of genetic recombination in bacteria characterized by DNA transfer from one organism called donor to another organism as recipient. This process occurs in three main ways:

<span class="mw-page-title-main">Double-strand break repair model</span>

A double-strand break repair model refers to the various models of pathways that cells undertake to repair double strand-breaks (DSB). DSB repair is an important cellular process, as the accumulation of unrepaired DSB could lead to chromosomal rearrangements, tumorigenesis or even cell death. In human cells, there are two main DSB repair mechanisms: Homologous recombination (HR) and non-homologous end joining (NHEJ). HR relies on undamaged template DNA as reference to repair the DSB, resulting in the restoration of the original sequence. NHEJ modifies and ligates the damaged ends regardless of homology. In terms of DSB repair pathway choice, most mammalian cells appear to favor NHEJ rather than HR. This is because the employment of HR may lead to gene deletion or amplification in cells which contains repetitive sequences. In terms of repair models in the cell cycle, HR is only possible during the S and G2 phases, while NHEJ can occur throughout whole process. These repair pathways are all regulated by the overarching DNA damage response mechanism. Besides HR and NHEJ, there are also other repair models which exists in cells. Some are categorized under HR, such as synthesis-dependent strain annealing, break-induced replication, and single-strand annealing; while others are an entirely alternate repair model, namely, the pathway microhomology-mediated end joining (MMEJ).

References

  1. ↑ Chen, Z.; Yang, H.; Pavletich, N. P. (2008). "Mechanism of homologous recombination from the RecA–ssDNA/dsDNA structures". Nature. 453 (7194): 489–4. Bibcode:2008Natur.453..489C. doi:10.1038/nature06971. PMID   18497818. S2CID   4416531.
  2. ↑ Horii, T; Ogawa, T; Ogawa, H (January 1980). "Organization of the recA gene of Escherichia coli". Proceedings of the National Academy of Sciences. 77 (1): 313–317. Bibcode:1980PNAS...77..313H. doi: 10.1073/pnas.77.1.313 . PMC   348260 . PMID   6244554.
  3. ↑ Lin, Zhenguo; Kong, Hongzhi; Nei, Masatoshi; Ma, Hong (5 July 2006). "Origins and evolution of the recA / RAD51 gene family: Evidence for ancient gene duplication and endosymbiotic gene transfer". Proceedings of the National Academy of Sciences. 103 (27): 10328–10333. Bibcode:2006PNAS..10310328L. doi: 10.1073/pnas.0604232103 . PMC   1502457 . PMID   16798872.
  4. ↑ Brendel, Volker; Brocchieri, Luciano; Sandler, Steven J.; Clark, Alvin J.; Karlin, Samuel (May 1997). "Evolutionary Comparisons of RecA-Like Proteins Across All Major Kingdoms of Living Organisms". Journal of Molecular Evolution. 44 (5): 528–541. doi:10.1007/pl00006177. PMID   9115177.
  5. ↑ Shinohara, Akira; Ogawa, Hideyuki; Ogawa, Tomoko (1992). "Rad51 protein involved in repair and recombination in S. cerevisiae is a RecA-like protein". Cell. 69 (3): 457–470. doi:10.1016/0092-8674(92)90447-k. PMID   1581961. S2CID   35937283.
  6. ↑ Seitz, Erica M.; Brockman, Joel P.; Sandler, Steven J.; Clark, A. John; Kowalczykowski, Stephen C. (1998-05-01). "RadA protein is an archaeal RecA protein homolog that catalyzes DNA strand exchange". Genes & Development. 12 (9): 1248–1253. doi:10.1101/gad.12.9.1248. ISSN   0890-9369. PMC   316774 . PMID   9573041.
  7. ↑ Horii, Toshihiro; Ogawa, Tomoko; Nakatani, Tomoyuki; Hase, Toshiharu; Matsubara, Hiroshi; Ogawa, Hideyuki (December 1981). "Regulation of SOS functions: Purification of E. coli LexA protein and determination of its specific site cleaved by the RecA protein". Cell. 27 (3): 515–522. doi:10.1016/0092-8674(81)90393-7. PMID   6101204. S2CID   45482725.
  8. ↑ Little, JW (March 1984). "Autodigestion of lexA and phage lambda repressors". Proceedings of the National Academy of Sciences. 81 (5): 1375–1379. Bibcode:1984PNAS...81.1375L. doi: 10.1073/pnas.81.5.1375 . PMC   344836 . PMID   6231641.
  9. 1 2 Henkin, Tina M.; Peters, Joseph E.; Snyder, Larry; Champness, Wendy (2020). Snyder & Champness molecular genetics of bacteria (Fifth ed.). Hoboken, NJ: Wiley. pp. 368–371. ISBN   9781555819750.
  10. ↑ Maraboeuf, Fabrice; Voloshin, Oleg; Camerini-Otero, R. Daniel; Takahashi, Masayuki (December 1995). "The Central Aromatic Residue in Loop L2 of RecA Interacts with DNA". Journal of Biological Chemistry. 270 (52): 30927–30932. doi: 10.1074/jbc.270.52.30927 . PMID   8537348.
  11. ↑ Wipperman, Matthew F.; Heaton, Brook E.; Nautiyal, Astha; Adefisayo, Oyindamola; Evans, Henry; Gupta, Richa; van Ditmarsch, Dave; Soni, Rajesh; Hendrickson, Ron; Johnson, Jeff; Krogan, Nevan; Glickman, Michael S. (October 2018). "Mycobacterial Mutagenesis and Drug Resistance Are Controlled by Phosphorylation- and Cardiolipin-Mediated Inhibition of the RecA Coprotease". Molecular Cell. 72 (1): 152–161.e7. doi:10.1016/j.molcel.2018.07.037. PMC   6389330 . PMID   30174294.
  12. ↑ Savir, Yonatan; Tlusty, Tsvi (November 2010). "RecA-Mediated Homology Search as a Nearly Optimal Signal Detection System". Molecular Cell. 40 (3): 388–396. arXiv: 1011.4382 . doi: 10.1016/j.molcel.2010.10.020 . PMID   21070965. S2CID   1682936.
  13. ↑ De Vlaminck, Iwijn; van Loenhout, Marjin T.J.; Zweifel, Ludovit; den Blanken, Johan; Hooning, Koen; Hage, Susanne; Kerssemakers, Jacob; Dekker, Cees (June 2012). "Mechanism of Homology Recognition in DNA Recombination from Dual-Molecule Experiments". Molecular Cell. 46 (5): 616–624. doi: 10.1016/j.molcel.2012.03.029 . PMID   22560720.
  14. ↑ Reitz, Diedre; Chan, Yuen-Ling; Bishop, Douglas K (December 2021). "How strand exchange protein function benefits from ATP hydrolysis". Current Opinion in Genetics & Development. 71: 120–128. doi:10.1016/j.gde.2021.06.016. PMC   8671154 . PMID   34343922.
  15. ↑ Lesterlin, Christian; Ball, Graeme; Schermelleh, Lothar; Sherratt, David J. (13 February 2014). "RecA bundles mediate homology pairing between distant sisters during DNA break repair". Nature. 506 (7487): 249–253. Bibcode:2014Natur.506..249L. doi:10.1038/nature12868. PMC   3925069 . PMID   24362571.
  16. ↑ Henkin, Tina M.; Peters, Joseph E.; Snyder, Larry; Champness, Wendy (2020). Snyder & Champness molecular genetics of bacteria (Fifth ed.). Hoboken, NJ: Wiley. p. 259. ISBN   9781555819750.
  17. ↑ Akamatsu, Takashi; Taguchi, Hisataka (January 2001). "Incorporation of the Whole Chromosomal DNA in Protoplast Lysates into Competent Cells of Bacillus subtilis". Bioscience, Biotechnology, and Biochemistry. 65 (4): 823–829. doi: 10.1271/bbb.65.823 . PMID   11388459. S2CID   30118947.
  18. ↑ Saito, Yukiko; Taguchi, Hisataka; Akamatsu, Takashi (March 2006). "Fate of transforming bacterial genome following incorporation into competent cells of Bacillus subtilis: a continuous length of incorporated DNA". Journal of Bioscience and Bioengineering. 101 (3): 257–262. doi:10.1263/jbb.101.257. PMID   16716928.
  19. 1 2 Culyba, Matthew J.; Mo, Charlie Y.; Kohli, Rahul M. (16 June 2015). "Targets for Combating the Evolution of Acquired Antibiotic Resistance". Biochemistry. 54 (23): 3573–3582. doi:10.1021/acs.biochem.5b00109. PMC   4471857 . PMID   26016604.
  20. ↑ Merrikh, Houra; Kohli, Rahul M. (October 2020). "Targeting evolution to inhibit antibiotic resistance". The FEBS Journal. 287 (20): 4341–4353. doi:10.1111/febs.15370. ISSN   1742-464X. PMC   7578009 . PMID   32434280.
  21. ↑ Wigle, Tim J.; Singleton, Scott F. (June 2007). "Directed molecular screening for RecA ATPase inhibitors". Bioorganic & Medicinal Chemistry Letters. 17 (12): 3249–3253. doi:10.1016/j.bmcl.2007.04.013. PMC   1933586 . PMID   17499507.
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