Escherichia coli K-12 substr. MG1655 Polypeptide: DNA mismatch endonuclease of the very short patch (VSP) mismatch repair pathway

Gene: vsr Accession Numbers: EG11068 (EcoCyc), b1960, ECK1958

Regulation Summary Diagram: ?

Regulation summary diagram for vsr

Vsr is an endonuclease that specifically recognizes and exhibits strand-specific nicking at T:G DNA mismatches, which arise from spontaneous deamination at 5-methylcytosine, the product of Dcm (cytosine) methylation [Hennecke91]. Vsr activity counterbalances the mutagenesis associated with dcm activity [Lieb91, Macintyre97].

Vsr is an essential component of the very short patch (VSP) mismatch repair pathway, as is PolA [Hennecke91], whereas MutL and MutS are involved but not essential [Hennecke91, Drotschmann98, Robertson12]. A minimal VSP pathway containing the purified components Vsr, PolA, DNA ligase I (LigA) and a plasmid substrate has been reconstituted in vitro [Robertson12]. Vsr binding to MutL antagonizes MutL homodimerization and decreases interactions among MutL, MutS, and MutH [Mansour01]. In vitro stimulation of Vsr requires MutS, MutL and ATP hydrolysis [Heinze09].

Crystal structures of Vsr are presented [Tsutakawa99, Bunting03]. Vsr substrate recognition and substrate specificity has been examined in detail [Glasner95, Lieb95, Tsutakawa99, Fox00, Turner00, GonzalezNicieza01, Bunting03].

A vsr mutation exhibits increased mutagenesis at the C2 of CCAGG sequences, compared to wild type [Ruiz93, Petropoulos94]. Vsr overproduction also results in increased mutagenesis [Doiron96, Macintyre97, Foster98].

Regulation has been described [Sohail90, Dar93, Macintyre99, Bell01]. The vsr and dcm genes overlap and are cotranscribed [Sohail90, Dar93]. However, abundance of the Dcm and Vsr proteins are subject to distinct regulation, and the abundance of Vsr is regulated by growth phase [Macintyre99]. The Dam (adenine) methylase affects regulation of Vsr abundance [Bell01].

Reviews: [Lieb96, Morikawa00, Cupples00, Bhagwat02, Tsutakawa00].

Citations: [Glasner92, Gabbara94, Aravind00, Lieb01, Takahashi02, Polosina09]

Locations: cytosol

Map Position: [2,028,472 <- 2,028,942] (43.72 centisomes, 157°)
Length: 471 bp / 156 aa

Molecular Weight of Polypeptide: 18.016 kD (from nucleotide sequence), 18 kD (experimental)

Unification Links: ASAP:ABE-0006507 , CGSC:28927 , DIP:DIP-11114N , EchoBASE:EB1061 , EcoGene:EG11068 , EcoliWiki:b1960 , ModBase:P09184 , OU-Microarray:b1960 , PortEco:vsr , PR:PRO_000024213 , Protein Model Portal:P09184 , RefSeq:NP_416469 , RegulonDB:EG11068 , SMR:P09184 , String:511145.b1960 , UniProt:P09184

Relationship Links: InterPro:IN-FAMILY:IPR004603 , InterPro:IN-FAMILY:IPR011335 , PDB:Structure:1CW0 , PDB:Structure:1ODG , PDB:Structure:1VSR , Pfam:IN-FAMILY:PF03852

GO Terms:

Biological Process: GO:0006298 - mismatch repair Inferred from experiment Inferred by computational analysis [GOA01a, Hennecke91]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Hennecke91]
GO:0006281 - DNA repair Inferred by computational analysis [UniProtGOA11a]
GO:0006974 - cellular response to DNA damage stimulus Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0003677 - DNA binding Inferred from experiment [Tsutakawa99]
GO:0005515 - protein binding Inferred from experiment [Polosina09a, Mansour01]
GO:0043765 - T/G mismatch-specific endonuclease activity Inferred from experiment [Hennecke91]
GO:0004518 - nuclease activity Inferred by computational analysis [UniProtGOA11a]
GO:0004519 - endonuclease activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer DNA related DNA repair

Essentiality data for vsr 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

Sequence Features

Protein sequence of DNA mismatch endonuclease of the very short patch (VSP) mismatch repair pathway with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
UniProt: Removed.
Chain 2 -> 156
UniProt: Very short patch repair protein;
Metal-Binding-Site 51
UniProt: Magnesium 1.
Metal-Binding-Site 63
UniProt: Magnesium 1.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b1960 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11068; confirmed by SwissProt match.


Aravind00: Aravind L, Makarova KS, Koonin EV (2000). "SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories." Nucleic Acids Res 2000;28(18);3417-32. PMID: 10982859

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

Bell01: Bell DC, Cupples CG (2001). "Very-short-patch repair in Escherichia coli requires the dam adenine methylase." J Bacteriol 183(12);3631-5. PMID: 11371527

Bhagwat02: Bhagwat AS, Lieb M (2002). "Cooperation and competition in mismatch repair: very short-patch repair and methyl-directed mismatch repair in Escherichia coli." Mol Microbiol 44(6);1421-8. PMID: 12067333

Bunting03: Bunting KA, Roe SM, Headley A, Brown T, Savva R, Pearl LH (2003). "Crystal structure of the Escherichia coli dcm very-short-patch DNA repair endonuclease bound to its reaction product-site in a DNA superhelix." Nucleic Acids Res 31(6);1633-9. PMID: 12626704

Cupples00: Cupples CG, Macintyre G (2000). "The E. coli Vsr endonuclease. Assaying activity in vitro and in vivo." Methods Mol Biol 152;63-73. PMID: 10957969

Dar93: Dar ME, Bhagwat AS (1993). "Mechanism of expression of DNA repair gene vsr, an Escherichia coli gene that overlaps the DNA cytosine methylase gene, dcm." Mol Microbiol 9(4);823-33. PMID: 7694036

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

Doiron96: Doiron KM, Viau S, Koutroumanis M, Cupples CG (1996). "Overexpression of vsr in Escherichia coli is mutagenic." J Bacteriol 178(14);4294-6. PMID: 8763960

Drotschmann98: Drotschmann K, Aronshtam A, Fritz HJ, Marinus MG (1998). "The Escherichia coli MutL protein stimulates binding of Vsr and MutS to heteroduplex DNA." Nucleic Acids Res 26(4);948-53. PMID: 9461452

Foster98: Foster PL, Rosche WA (1998). "Levels of the Vsr endonuclease do not regulate stationary-phase reversion of a Lac- frameshift allele in Escherichia coli." J Bacteriol 180(7);1944-6. PMID: 9537396

Fox00: Fox KR, Allinson SL, Sahagun-Krause H, Brown T (2000). "Recognition of GT mismatches by Vsr mismatch endonuclease." Nucleic Acids Res 28(13);2535-40. PMID: 10871403

Gabbara94: Gabbara S, Wyszynski M, Bhagwat AS (1994). "A DNA repair process in Escherichia coli corrects U:G and T:G mismatches to C:G at sites of cytosine methylation." Mol Gen Genet 243(2);244-8. PMID: 8177221

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

Glasner92: Glasner W, Merkl R, Schmidt S, Cech D, Fritz HJ (1992). "Fast quantitative assay of sequence-specific endonuclease activity based on DNA sequencer technology." Biol Chem Hoppe Seyler 373(12);1223-5. PMID: 1337970

Glasner95: Glasner W, Merkl R, Schellenberger V, Fritz HJ (1995). "Substrate preferences of Vsr DNA mismatch endonuclease and their consequences for the evolution of the Escherichia coli K-12 genome." J Mol Biol 245(1);1-7. PMID: 7823316

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GonzalezNicieza01: Gonzalez-Nicieza R, Turner DP, Connolly BA (2001). "DNA binding and cleavage selectivity of the Escherichia coli DNA G:T-mismatch endonuclease (vsr protein)." J Mol Biol 310(3);501-8. PMID: 11439018

Heinze09: Heinze RJ, Giron-Monzon L, Solovyova A, Elliot SL, Geisler S, Cupples CG, Connolly BA, Friedhoff P (2009). "Physical and functional interactions between Escherichia coli MutL and the Vsr repair endonuclease." Nucleic Acids Res 37(13):4453-63. PMID: 19474347

Hennecke91: Hennecke F, Kolmar H, Brundl K, Fritz HJ (1991). "The vsr gene product of E. coli K-12 is a strand- and sequence-specific DNA mismatch endonuclease." Nature 353(6346);776-8. PMID: 1944537

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

Lieb01: Lieb M, Rehmat S, Bhagwat AS (2001). "Interaction of MutS and Vsr: some dominant-negative mutS mutations that disable methyladenine-directed mismatch repair are active in very-short-patch repair." J Bacteriol 183(21);6487-90. PMID: 11591694

Lieb91: Lieb M (1991). "Spontaneous mutation at a 5-methylcytosine hotspot is prevented by very short patch (VSP) mismatch repair." Genetics 1991;128(1);23-7. PMID: 1829427

Lieb95: Lieb M, Rehmat S (1995). "Very short patch repair of T:G mismatches in vivo: importance of context and accessory proteins." J Bacteriol 177(3);660-6. PMID: 7836300

Lieb96: Lieb M, Bhagwat AS (1996). "Very short patch repair: reducing the cost of cytosine methylation." Mol Microbiol 1996;20(3);467-73. PMID: 8736526

Macintyre97: Macintyre G, Doiron KM, Cupples CG (1997). "The Vsr endonuclease of Escherichia coli: an efficient DNA repair enzyme and a potent mutagen." J Bacteriol 179(19);6048-52. PMID: 9324251

Macintyre99: Macintyre G, Pitsikas P, Cupples CG (1999). "Growth phase-dependent regulation of Vsr endonuclease may contribute to 5-methylcytosine mutational hot spots in Escherichia coli." J Bacteriol 181(14);4435-6. PMID: 10400606

Mansour01: Mansour CA, Doiron KM, Cupples CG (2001). "Characterization of functional interactions among the Escherichia coli mismatch repair proteins using a bacterial two-hybrid assay." Mutat Res 485(4);331-8. PMID: 11585365

Morikawa00: Morikawa K, Shirakawa M (2000). "Three-dimensional structural views of damaged-DNA recognition: T4 endonuclease V, E. coli Vsr protein, and human nucleotide excision repair factor XPA." Mutat Res 460(3-4);257-75. PMID: 10946233

Petropoulos94: Petropoulos L, Vidmar JJ, Passi E, Cupples CG (1994). "A simple assay for monitoring the mutagenic effects of 5-methylcytosine deamination in Escherichia coli." Mutat Res 304(2);181-5. PMID: 7506360

Polosina09: Polosina YY, Cupples CG (2009). "Changes in the conformation of the Vsr endonuclease amino-terminal domain accompany DNA cleavage." J Biochem. PMID: 19556224

Polosina09a: Polosina YY, Mui J, Pitsikas P, Cupples CG (2009). "The Escherichia coli mismatch repair protein MutL recruits the Vsr and MutH endonucleases in response to DNA damage." J Bacteriol 191(12);4041-3. PMID: 19376855

Robertson12: Robertson AB, Matson SW (2012). "Reconstitution of the Very Short Patch Repair Pathway from Escherichia coli." J Biol Chem. PMID: 22846989

Ruiz93: Ruiz SM, Letourneau S, Cupples CG (1993). "Isolation and characterization of an Escherichia coli strain with a high frequency of C-to-T mutations at 5-methylcytosines." J Bacteriol 175(16);4985-9. PMID: 8349541

Sohail90: Sohail A, Lieb M, Dar M, Bhagwat AS (1990). "A gene required for very short patch repair in Escherichia coli is adjacent to the DNA cytosine methylase gene." J Bacteriol 172(8);4214-21. PMID: 2198248

Takahashi02: Takahashi N, Naito Y, Handa N, Kobayashi I (2002). "A DNA methyltransferase can protect the genome from postdisturbance attack by a restriction-modification gene complex." J Bacteriol 184(22);6100-8. PMID: 12399478

Tsutakawa00: Tsutakawa SE, Morikawa K (2000). "New recognition mode for a TG mismatch: the atomic structure of a very short patch repair endonuclease-DNA complex." Cold Spring Harb Symp Quant Biol 65;233-9. PMID: 12760037

Tsutakawa99: Tsutakawa SE, Jingami H, Morikawa K (1999). "Recognition of a TG mismatch: the crystal structure of very short patch repair endonuclease in complex with a DNA duplex." Cell 99(6);615-23. PMID: 10612397

Turner00: Turner DP, Connolly BA (2000). "Interaction of the E. coli DNA G:T-mismatch endonuclease (vsr protein) with oligonucleotides containing its target sequence." J Mol Biol 304(5);765-78. PMID: 11124025

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

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

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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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