Escherichia coli K-12 substr. MG1655 Enzyme: toxin of the YafQ-DinJ toxin-antitoxin system

Gene: yafQ Accession Numbers: G6109 (EcoCyc), b0225, ECK0226

Regulation Summary Diagram: ?

Regulation summary diagram for yafQ

Component of: DinJ-YafQ antitoxin/toxin complex and DNA-binding transcriptional repressor (extended summary available)

YafQ acts as a toxin by inhibiting translation; it interacts with the 50S subunit of the ribosome and cleaves mRNAs at AAA codons. Interaction with its cognate antitoxin, DinJ, abolishes RNase activity of YafQ [Prysak09].

YafQ shows structual similarity to ribunucleases and the YoeB toxin, but several conserved catalytic residues are not conserved in YafQ [Motiejunaite07].

Surprisingly, overexpression of yafQ in liquid medium has no deleterious effect, while overexpression on solid medium inhibits growth [KolodkinGal09].

Although a yafQ deletion mutant produces biofilms with wild type appearance, the biofilms show up to a 2,400-fold decrease in survival after exposure to the antibiotics cefazolin or tobramycin. Overexpression of yafQ results in increased survival of biofilm cells under those conditions. The effect is specific to biofilm growth conditions and the antibiotic used; no effect on tolerance is seen with deoxycycline or rifampicin and under stationary phase planktonic growth conditions [Harrison09].

Review: [Yamaguchi11]

Map Position: [245,961 <- 246,239] (5.3 centisomes, 19°)
Length: 279 bp / 92 aa

Molecular Weight of Polypeptide: 10.847 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0000761 , DIP:DIP-11221N , EchoBASE:EB2948 , EcoGene:EG13154 , EcoliWiki:b0225 , Mint:MINT-1263057 , OU-Microarray:b0225 , PortEco:yafQ , Protein Model Portal:Q47149 , RefSeq:NP_414760 , RegulonDB:G6109 , SMR:Q47149 , String:511145.b0225 , Swiss-Model:Q47149 , UniProt:Q47149

Relationship Links: InterPro:IN-FAMILY:IPR004386 , InterPro:IN-FAMILY:IPR007712 , PDB:Structure:4ML2 , PDB:Structure:4MMG , PDB:Structure:4Q2U

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for yafQ

GO Terms:

Biological Process: GO:0006402 - mRNA catabolic process Inferred from experiment [Prysak09]
GO:0006415 - translational termination Inferred from experiment [Prysak09]
GO:0044010 - single-species biofilm formation Inferred from experiment [KolodkinGal09]
GO:0046677 - response to antibiotic Inferred from experiment [Harrison09]
GO:0090502 - RNA phosphodiester bond hydrolysis, endonucleolytic Inferred from experiment [Prysak09]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0004521 - endoribonuclease activity Inferred from experiment [Prysak09]
GO:0005515 - protein binding Inferred from experiment [Motiejunaite07]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0004518 - nuclease activity Inferred by computational analysis [UniProtGOA11]
GO:0004519 - endonuclease activity Inferred by computational analysis [UniProtGOA11]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell processes protection cell killing

Essentiality data for yafQ knockouts: ?

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

Last-Curated ? 30-Mar-2009 by Keseler I , SRI International

Enzymatic reaction of: RNase (toxin of the YafQ-DinJ toxin-antitoxin system)

EC Number: 3.1.26.-

an mRNA + H2O <=> a single-stranded RNA + a single-stranded RNA

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.

Subunit of: DinJ-YafQ antitoxin/toxin complex and DNA-binding transcriptional repressor

Synonyms: DinJ/Q

Subunit composition of DinJ-YafQ antitoxin/toxin complex and DNA-binding transcriptional repressor = [YafQ][DinJ]
         toxin of the YafQ-DinJ toxin-antitoxin system = YafQ (extended summary available)
         DinJ antitoxin of YafQ-DinJ toxin-antitoxin system and DNA-binding transcriptional repressor = DinJ (extended summary available)

The YafQ-DinJ toxin-antitoxin system was identified by its similarity to the RelE-RelB toxin-antitoxin system [Gotfredsen98]. Expression of YafQ alone reduces protein synthesis and inhibits growth, and coexpression of DinJ alleviates that phenotype, acting as the antitoxin [Motiejunaite07, Szekeres07, Prysak09].

YafQ and DinJ form a stable complex [Motiejunaite07] which can bind to the dinJ-yafQ palindrome upstream of the translation start site [Prysak09].

A strain from which all five toxin-antitoxin systems have been deleted shows no deficiency in its stress response or competitiveness under nutrient-limited conditions [Tsilibaris07]. However, biofilm formation is affected via expression of the TabA protein [Kim09b]. A dinJ-yafQ deletion mutant is impaired in biofilm formation [KolodkinGal09].

Deletion of any single toxin-antitoxin system encoding an RNase has no effect on persister formation, but deleting ten such systems dramatically reduces persister formation. Persister formation depends on degradation of the antitoxins by the Lon protease [Maisonneuve11].

A crystal structure of the DinJ-YafQ complex has been resolved at 1.8 Å [Ruangprasert14].

Reviews: [Gerdes00, Buts05, Gerdes05, Condon06, Inouye06, Magnuson07]

GO Terms:

Molecular Function: GO:0043565 - sequence-specific DNA binding Inferred from experiment [Prysak09]

Created 18-Mar-2009 by Keseler I , SRI International
Last-Curated ? 18-Mar-2009 by Keseler I , SRI International

DNA binding site length: 16 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: CTGnATAnnTATnCAG

Regulated Transcription Units (2 total): ?


Transcription-unit diagram

Transcription-unit diagram

Sequence Features

Protein sequence of toxin of the YafQ-DinJ toxin-antitoxin system with features indicated

Feature Class Location Citations Comment
Mutagenesis-Variant 87
[Prysak09, UniProt11]
UniProt: Loss of mRNA cleavage, loss of toxic effect. Still associates with the ribosome.
Active-Site 87
UniProt: Proton donor; Non-Experimental Qualifier: probable.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

Buts05: Buts L, Lah J, Dao-Thi MH, Wyns L, Loris R (2005). "Toxin-antitoxin modules as bacterial metabolic stress managers." Trends Biochem Sci 30(12);672-9. PMID: 16257530

Condon06: Condon C (2006). "Shutdown decay of mRNA." Mol Microbiol 61(3);573-83. PMID: 16803593

Gerdes00: Gerdes K (2000). "Toxin-antitoxin modules may regulate synthesis of macromolecules during nutritional stress." J Bacteriol 182(3);561-72. PMID: 10633087

Gerdes05: Gerdes K, Christensen SK, Lobner-Olesen A (2005). "Prokaryotic toxin-antitoxin stress response loci." Nat Rev Microbiol 3(5);371-82. PMID: 15864262

Gotfredsen98: Gotfredsen M, Gerdes K (1998). "The Escherichia coli relBE genes belong to a new toxin-antitoxin gene family." Mol Microbiol 29(4);1065-76. PMID: 9767574

Harrison09: Harrison JJ, Wade WD, Akierman S, Vacchi-Suzzi C, Stremick CA, Turner RJ, Ceri H (2009). "The chromosomal toxin yafQ is a determinant of multidrug tolerance for Escherichia coli growing in a biofilm." Antimicrob Agents Chemother 53(6):2253-8. PMID: 19307375

Inouye06: Inouye M (2006). "The discovery of mRNA interferases: implication in bacterial physiology and application to biotechnology." J Cell Physiol 209(3);670-6. PMID: 17001682

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

Kim09b: Kim Y, Wang X, Ma Q, Zhang XS, Wood TK (2009). "Toxin-Antitoxin Systems in Escherichia coli Influence Biofilm Formation Through YjgK (TabA) and Fimbriae." J Bacteriol 191(4):1258-67. PMID: 19060153

KolodkinGal09: Kolodkin-Gal I, Verdiger R, Shlosberg-Fedida A, Engelberg-Kulka H (2009). "A differential effect of E. coli toxin-antitoxin systems on cell death in liquid media and biofilm formation." PLoS One 4(8);e6785. PMID: 19707553

Magnuson07: Magnuson RD (2007). "Hypothetical functions of toxin-antitoxin systems." J Bacteriol 189(17);6089-92. PMID: 17616596

Maisonneuve11: Maisonneuve E, Shakespeare LJ, Jorgensen MG, Gerdes K (2011). "Bacterial persistence by RNA endonucleases." Proc Natl Acad Sci U S A 108(32);13206-11. PMID: 21788497

Motiejunaite07: Motiejunaite R, Armalyte J, Markuckas A, Suziedeliene E (2007). "Escherichia coli dinJ-yafQ genes act as a toxin-antitoxin module." FEMS Microbiol Lett 268(1);112-9. PMID: 17263853

Prysak09: Prysak MH, Mozdzierz CJ, Cook AM, Zhu L, Zhang Y, Inouye M, Woychik NA (2009). "Bacterial toxin YafQ is an endoribonuclease that associates with the ribosome and blocks translation elongation through sequence-specific and frame-dependent mRNA cleavage." Mol Microbiol 71(5);1071-87. PMID: 19210620

Ruangprasert14: Ruangprasert A, Maehigashi T, Miles SJ, Giridharan N, Liu JX, Dunham CM (2014). "Mechanisms of toxin inhibition and transcriptional repression by Escherichia coli DinJ-YafQ." J Biol Chem 289(30);20559-69. PMID: 24898247

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

Szekeres07: Szekeres S, Dauti M, Wilde C, Mazel D, Rowe-Magnus DA (2007). "Chromosomal toxin-antitoxin loci can diminish large-scale genome reductions in the absence of selection." Mol Microbiol 63(6);1588-605. PMID: 17367382

Tsilibaris07: Tsilibaris V, Maenhaut-Michel G, Mine N, Van Melderen L (2007). "What is the benefit to Escherichia coli of having multiple toxin-antitoxin systems in its genome?." J Bacteriol 189(17);6101-8. PMID: 17513477

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

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

Yamaguchi11: Yamaguchi Y, Park JH, Inouye M (2011). "Toxin-antitoxin systems in bacteria and archaea." Annu Rev Genet 45;61-79. PMID: 22060041

Other References Related to Gene Regulation

Huerta03: Huerta AM, Collado-Vides J (2003). "Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals." J Mol Biol 333(2);261-78. PMID: 14529615

Lewis94: Lewis LK, Harlow GR, Gregg-Jolly LA, Mount DW (1994). "Identification of high affinity binding sites for LexA which define new DNA damage-inducible genes in Escherichia coli." J Mol Biol 241(4);507-23. PMID: 8057377

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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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