Escherichia coli K-12 substr. MG1655 Polypeptide: regulatory protein RecX; inhibitor of RecA

Gene: recX Accession Numbers: EG12080 (EcoCyc), b2698, ECK2693

Synonyms: oraA

Regulation Summary Diagram: ?

Regulation summary diagram for recX

RecX is an inhibitor of RecA. RecX interacts directly with RecA, inhibits its ssDNA-dependent ATPase, coprotease, and DNA strand exchange activities [Stohl03, Drees04], and blocks the extension of RecA filaments [Drees04a] or promotes RecA filament disassembly [Ragone08]. RecX itself has weak ssDNA binding activity [Drees04a]; functional competition between SSB and RecX suggest that an interaction of RecX with ssDNA may be part of the mechanism by which RecX inhibits RecA [Baitin08].

The interaction between RecX and RecA itself is modulated by other proteins. RecX competes directly with DinI, a positive modulator of RecA function, for binding to RecA [Lusetti04]. Both proteins modulate RecA-DNA structures, with dinI being epistatic to recX, wich is consistent with DinI acting upstream of RecX [Renzette07]. RecF protects nucleated RecA filaments from RecX inhibition [Lusetti06].

A structural model of RecX has been proposed, and its interaction with RecA [Mishra03] and ssDNA [Shvetsov14] was modeled. The interaction between RecX and RecA is modulated by the C-terminal domain of RecA and the concentration of free Mg2+ [Drees04, Renzette07]. A crystal structure of RecX from E. coli E24377A (99% sequence identity with the E. coli K-12 protein) has been solved at 1.8 Å resolution, showing a modular protein with repeated three-helix motifs. Site-directed mutagenesis of conserved basic residues on the concave side of RecX showed that they are important for repression of RecA activity in vitro [Ragone08].

Transcription of recX is regulated by LexA [Stohl03]. Expression is induced by DNA damage [Stohl03], nalidixic acid or mitomycin C [Van01]. Although recA and recX are cotranscribed, RecX is approximately 500 times less abundant than RecA. SOS transcriptional regulation and a translational regulation process each contribute to regulation of RecX abundance [Pages03].

Overproduction of RecX causes UV sensitivity and additional phenotypes that are consistent with RecA inhibition, such as defects in DNA damage induction of transcription and proteolysis of UmuD and LexA, and less P1 transduction compared to wild type [Stohl03]. Published reports differ as to whether there is a small [Stohl03, Renzette07] or no [Pages03] difference in UV sensitivity of a recX null mutant compared to wild type. A null mutation does not cause increased mutagenesis [Pages03], defects in DNA damage induction of transcription and proteolysis of UmuD and LexA [Stohl03], or defects in P1 transduction [Stohl03]. Overproduction of RecA is not lethal in a recX null mutant background, in contrast to the situation observed in other organisms [Pages03]. RecX does not appear to regulate transcription of recA [Pages03]. In wild-type cells, RecX itself does not appear to play a significant role in repression of SOS expression [Massoni12].

Review: [Cox07]

Citations: [Zaitsev94, De94, Stohl02, Long08a, Long09, Bakhlanova10, Dudkina, Moore12, Venkatesh02]

Locations: cytosol

Map Position: [2,820,161 <- 2,820,661] (60.78 centisomes, 219°)
Length: 501 bp / 166 aa

Molecular Weight of Polypeptide: 19.424 kD (from nucleotide sequence), 19.274 kD (experimental) [Drees04 ]

Unification Links: ASAP:ABE-0008872 , DIP:DIP-10410N , EchoBASE:EB2005 , EcoGene:EG12080 , EcoliWiki:b2698 , OU-Microarray:b2698 , PortEco:recX , PR:PRO_000023709 , Protein Model Portal:P33596 , RefSeq:NP_417178 , RegulonDB:EG12080 , SMR:P33596 , String:511145.b2698 , UniProt:P33596

Relationship Links: InterPro:IN-FAMILY:IPR003783 , InterPro:IN-FAMILY:IPR011991 , PDB:Structure:2A7Z , Pfam:IN-FAMILY:PF02631

Genetic Regulation Schematic: ?

Genetic regulation schematic for recX

GO Terms:

Biological Process: GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment Inferred by computational analysis [UniProtGOA11, Stohl03]
GO:0009432 - SOS response Inferred from experiment Inferred by computational analysis [UniProtGOA11, Stohl03]
GO:0043086 - negative regulation of catalytic activity Inferred from experiment [Stohl03]
GO:0006281 - DNA repair Inferred by computational analysis [UniProtGOA11]
GO:0006282 - regulation of DNA repair Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Lusetti06]
GO:0019899 - enzyme binding Inferred from experiment [Stohl03]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell processes protection radiation
cell processes SOS response
information transfer DNA related DNA recombination
information transfer DNA related DNA repair
regulation type of regulation posttranscriptional inhibition / activation of enzymes

Essentiality data for recX knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Last-Curated ? 30-Apr-2014 by Keseler I , SRI International

Sequence Features

Protein sequence of regulatory protein RecX; inhibitor of RecA with features indicated

Feature Class Location Citations Comment
Sequence-Conflict 19
[Zaitsev94, UniProt10a]
UniProt: (in Ref. 1; AAA19106);
Sequence-Conflict 120
[Zaitsev94, UniProt10a]
UniProt: (in Ref. 1; AAA19106);

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b2698 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12080; confirmed by SwissProt match.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Baitin08: Baitin DM, Gruenig MC, Cox MM (2008). "SSB antagonizes RecX-RecA interaction." J Biol Chem 283(21);14198-204. PMID: 18385131

Bakhlanova10: Bakhlanova IV, Dudkina AV, Baitin DM, Knight KL, Cox MM, Lanzov VA (2010). "Modulating cellular recombination potential through alterations in RecA structure and regulation." Mol Microbiol 78(6);1523-38. PMID: 21143322

Cox07: Cox MM (2007). "Regulation of bacterial RecA protein function." Crit Rev Biochem Mol Biol 42(1);41-63. PMID: 17364684

De94: De Mot R, Schoofs G, Vanderleyden J (1994). "A putative regulatory gene downstream of recA is conserved in gram-negative and gram-positive bacteria." Nucleic Acids Res 22(7);1313-4. PMID: 8165147

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Drees04: Drees JC, Lusetti SL, Cox MM (2004). "Inhibition of RecA protein by the Escherichia coli RecX protein: modulation by the RecA C terminus and filament functional state." J Biol Chem 279(51);52991-7. PMID: 15466870

Drees04a: Drees JC, Lusetti SL, Chitteni-Pattu S, Inman RB, Cox MM (2004). "A RecA filament capping mechanism for RecX protein." Mol Cell 15(5);789-98. PMID: 15350222

Dudkina: Dudkina AV, Shvetsov AV, Bakhlanova IV, Baitin DM "[Changing of filamentation dynamics of RecA protein, induced by D112R amino acid substitution or ATP to dATP replacement, results in filament steadiness TO THE RecX protein action]." Mol Biol (Mosk) 45(3);546-53. PMID: 21790018

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Long08a: Long JE, Renzette N, Centore RC, Sandler SJ (2008). "Differential requirements of two recA mutants for constitutive SOS expression in Escherichia coli K-12." PLoS One 3(12);e4100. PMID: 19116657

Long09: Long JE, Renzette N, Sandler SJ (2009). "Suppression of constitutive SOS expression by recA4162 (I298V) and recA4164 (L126V) requires UvrD and RecX in Escherichia coli K-12." Mol Microbiol 73(2);226-39. PMID: 19555451

Lusetti04: Lusetti SL, Drees JC, Stohl EA, Seifert HS, Cox MM (2004). "The DinI and RecX proteins are competing modulators of RecA function." J Biol Chem 279(53);55073-9. PMID: 15489505

Lusetti06: Lusetti SL, Hobbs MD, Stohl EA, Chitteni-Pattu S, Inman RB, Seifert HS, Cox MM (2006). "The RecF protein antagonizes RecX function via direct interaction." Mol Cell 21(1);41-50. PMID: 16387652

Massoni12: Massoni SC, Leeson MC, Long JE, Gemme K, Mui A, Sandler SJ (2012). "Factors limiting SOS expression in log-phase cells of Escherichia coli." J Bacteriol 194(19);5325-33. PMID: 22843848

Mishra03: Mishra S, Mazumdar PA, Dey J, Das AK (2003). "Molecular modeling of RecX reveals its mode of interaction with RecA." Biochem Biophys Res Commun 312(3);615-22. PMID: 14680809

Moore12: Moore JM, Wimberly H, Thornton PC, Rosenberg SM, Hastings PJ (2012). "Gross chromosomal rearrangement mediated by DNA replication in stressed cells: evidence from Escherichia coli." Ann N Y Acad Sci 1267;103-9. PMID: 22954223

Pages03: Pages V, Koffel-Schwartz N, Fuchs RP (2003). "recX, a new SOS gene that is co-transcribed with the recA gene in Escherichia coli." DNA Repair (Amst) 2003;2(3);273-84. PMID: 12547390

Ragone08: Ragone S, Maman JD, Furnham N, Pellegrini L (2008). "Structural basis for inhibition of homologous recombination by the RecX protein." EMBO J 27(16);2259-69. PMID: 18650935

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Renzette07: Renzette N, Gumlaw N, Sandler SJ (2007). "DinI and RecX modulate RecA-DNA structures in Escherichia coli K-12." Mol Microbiol 63(1);103-15. PMID: 17163974

Shvetsov14: Shvetsov AV, Lebedev DV, Chervyakova DB, Bakhlanova IV, Yung IA, Radulescu A, Kuklin AI, Baitin DM, Isaev-Ivanov VV (2014). "Structure of RecX protein complex with the presynaptic RecA filament: Molecular dynamics simulations and small angle neutron scattering." FEBS Lett 588(6);948-55. PMID: 24530684

Stohl02: Stohl EA, Blount L, Seifert HS (2002). "Differential cross-complementation patterns of Escherichia coli and Neisseria gonorrhoeae RecA proteins." Microbiology 2002;148(Pt 6);1821-31. PMID: 12055302

Stohl03: Stohl EA, Brockman JP, Burkle KL, Morimatsu K, Kowalczykowski SC, Seifert HS (2003). "Escherichia coli RecX inhibits RecA recombinase and coprotease activities in vitro and in vivo." J Biol Chem 2003;278(4);2278-85. PMID: 12427742

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

Van01: Van Dyk TK, DeRose EJ, Gonye GE (2001). "LuxArray, a high-density, genomewide transcription analysis of Escherichia coli using bioluminescent reporter strains." J Bacteriol 183(19);5496-505. PMID: 11544210

Venkatesh02: Venkatesh R, Ganesh N, Guhan N, Reddy MS, Chandrasekhar T, Muniyappa K (2002). "RecX protein abrogates ATP hydrolysis and strand exchange promoted by RecA: insights into negative regulation of homologous recombination." Proc Natl Acad Sci U S A 2002;99(19);12091-6. PMID: 12218174

Zaitsev94: Zaitsev E, Alexseyev A, Lanzov V, Satin L, Clark AJ (1994). "Nucleotide sequence between recA and alaSp in E. coli K12 and the sequence change in four recA mutations." Mutat Res 1994;323(4);173-7. PMID: 7512687

Other References Related to Gene Regulation

Brent81: Brent R, Ptashne M (1981). "Mechanism of action of the lexA gene product." Proc Natl Acad Sci U S A 1981;78(7);4204-8. PMID: 7027256

Little81: Little JW, Mount DW, Yanisch-Perron CR (1981). "Purified lexA protein is a repressor of the recA and lexA genes." Proc Natl Acad Sci U S A 1981;78(7);4199-203. PMID: 7027255

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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