Escherichia coli K-12 substr. MG1655 Enzyme: exonuclease VIII, ds DNA exonuclease, 5' --> 3' specific

Gene: recE Accession Numbers: EG10827 (EcoCyc), b1350, ECK1347

Synonyms: rmuB, rac, sbcA

Regulation Summary Diagram: ?

Regulation summary diagram for recE

DNA damage can occur due to a variety of environmental assaults including UV irradiation and chemical agents. Escherichia coli has a number of complex enzymatic pathways for the repair of DNA damage. Most DNA damage involves lesions to one strand of DNA, but in some cases damage can occur to both strands. Double strand breaks (DSBs) cannot be repaired via excision repair pathways because by their nature they lack an intact strand to be used as a template. Repair of DSBs utilize the RecA pathway of homologous recombination with a separate, intact, homologous region of DNA.

The RecE (also known as exonuclease VIII) pathway is an alternative pathway for the initiation of homologous recombination in Escherichia coli. The RecE pathway is activated in recB, recC sbcA (suppressors of recB and recC) mutants. Activation of the RecE pathway results in the production of at least two phage proteins relevant for recombinational repair. RecE is a duplex DNA-specific exonuclease which produces 3' overhangs in duplex DNA by preferentially degrading the 5'-ending strands [Kuzminov99, Joseph83]. RecT promotes the annealing of complementary single strands and can also catalyze three-strand recombinational junction branch migration [Kuzminov99].

The crystal structure of the C-terminal nuclease domain of RecE has been resolved at 2.8Å resolution [Zhang09d]. The RecE C-terminal domain comprising amino acid residues 606-866 forms a stable tetramer in solution [Zhang09d].

Recombinational repair of E. coli chromosomal DNA requires-- in addition to RecE and RecT-- RecA, RecF, RecJ, RecO, RecR, and RuvC [Kuzminov99, Gillen81, Clark93, Ishioka97].

recE transcription is increased specifically in response to 2,4,6-trinitrotoluene and its indicator compounds 1,3-DNB, 2,4-DNT, and 2,6-DNT; the response was utilized for construction of an E. coli biosensor strain [Tan15].

Map Position: [1,412,810 <- 1,415,410] (30.45 centisomes, 110°)
Length: 2601 bp / 866 aa

Molecular Weight of Polypeptide: 96.368 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0004531 , CGSC:309 , DIP:DIP-10652N , EchoBASE:EB0820 , EcoGene:EG10827 , EcoliWiki:b1350 , Mint:MINT-1262359 , OU-Microarray:b1350 , PortEco:recE , PR:PRO_000023700 , Pride:P15032 , Protein Model Portal:P15032 , RefSeq:NP_415866 , RegulonDB:EG10827 , SMR:P15032 , String:511145.b1350 , UniProt:P15032

Relationship Links: InterPro:IN-FAMILY:IPR010584 , InterPro:IN-FAMILY:IPR024432 , PDB:Structure:3H4R , Pfam:IN-FAMILY:PF06630 , Pfam:IN-FAMILY:PF12684

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for recE

GO Terms:

Biological Process: GO:0006259 - DNA metabolic process Inferred from experiment [Joseph83]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis Inferred by computational analysis Inferred from experiment [Joseph83, UniProtGOA11]
GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0051908 - double-stranded DNA 5'-3' exodeoxyribonuclease activity Inferred from experiment [Joseph83]
GO:0004518 - nuclease activity Inferred by computational analysis [UniProtGOA11]
GO:0004527 - exonuclease activity Inferred by computational analysis [UniProtGOA11]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: extrachromosomal prophage genes and phage related functions
information transfer DNA related DNA degradation
information transfer DNA related DNA repair
metabolism degradation of macromolecules DNA

Essentiality data for recE 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 ? 26-Jul-2009 by Mackie A , Macquarie University

Enzymatic reaction of: DNA exonuclease

EC Number: 3.1.11.-

a double stranded DNA + H2O <=> a single stranded DNA + a 5'-phosphomononucleotide

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Sequence Features

Protein sequence of exonuclease VIII, ds DNA exonuclease, 5' --> 3' specific with features indicated

Feature Class Location Citations Comment
Sequence-Conflict 366
[Chu89, UniProt10a]
UniProt: (in Ref. 4; AAA03212);
Sequence-Conflict 691 -> 692
[Clark93, UniProt10a]
UniProt: (in Ref. 6);

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b1350 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10827; 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

Chu89: Chu CC, Templin A, Clark AJ (1989). "Suppression of a frameshift mutation in the recE gene of Escherichia coli K-12 occurs by gene fusion." J Bacteriol 171(4);2101-9. PMID: 2649487

Clark93: Clark AJ, Sharma V, Brenowitz S, Chu CC, Sandler S, Satin L, Templin A, Berger I, Cohen A (1993). "Genetic and molecular analyses of the C-terminal region of the recE gene from the Rac prophage of Escherichia coli K-12 reveal the recT gene." J Bacteriol 175(23);7673-82. PMID: 8244937

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

Gillen81: Gillen JR, Willis DK, Clark AJ (1981). "Genetic analysis of the RecE pathway of genetic recombination in Escherichia coli K-12." J Bacteriol 145(1);521-32. PMID: 6257642

Ishioka97: Ishioka K, Iwasaki H, Shinagawa H (1997). "Roles of the recG gene product of Escherichia coli in recombination repair: effects of the delta recG mutation on cell division and chromosome partition." Genes Genet Syst 72(2);91-9. PMID: 9265736

Joseph83: Joseph JW, Kolodner R (1983). "Exonuclease VIII of Escherichia coli. II. Mechanism of action." J Biol Chem 258(17);10418-24. PMID: 6309804

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

Kuzminov99: Kuzminov A (1999). "Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda." Microbiol Mol Biol Rev 63(4);751-813, table of contents. PMID: 10585965

Tan15: Tan J, Kan N, Wang W, Ling J, Qu G, Jin J, Shao Y, Liu G, Chen H (2015). "Construction of 2,4,6-Trinitrotoluene Biosensors with Novel Sensing Elements from Escherichia coli K-12 MG1655." Cell Biochem Biophys. PMID: 25561288

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."

Zhang09d: Zhang J, Xing X, Herr AB, Bell CE (2009). "Crystal structure of E. coli RecE protein reveals a toroidal tetramer for processing double-stranded DNA breaks." Structure 17(5);690-702. PMID: 19446525

Other References Related to Gene Regulation

Guo14a: Guo Y, Quiroga C, Chen Q, McAnulty MJ, Benedik MJ, Wood TK, Wang X (2014). "RalR (a DNase) and RalA (a small RNA) form a type I toxin-antitoxin system in Escherichia coli." Nucleic Acids Res 42(10);6448-62. PMID: 24748661

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Tue Oct 6, 2015, biocyc13.