|Gene:||yafQ||Accession Numbers: G6109 (EcoCyc), b0225, ECK0226|
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 [KolodkinGal09a].
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].
|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
|Biological Process:||GO:0006402 - mRNA catabolic process
GO:0006415 - translational termination [Prysak09]
GO:0044010 - single-species biofilm formation [KolodkinGal09a]
GO:0046677 - response to antibiotic [Harrison09]
GO:0090502 - RNA phosphodiester bond hydrolysis, endonucleolytic [Prysak09]
GO:0006351 - transcription, DNA-templated [UniProtGOA11a]
GO:0006355 - regulation of transcription, DNA-templated [UniProtGOA11a]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis [UniProtGOA11a]
|Molecular Function:||GO:0004521 - endoribonuclease activity
GO:0005515 - protein binding [Motiejunaite07]
GO:0003677 - DNA binding [UniProtGOA11a]
GO:0003723 - RNA binding [UniProtGOA11a]
GO:0004518 - nuclease activity [UniProtGOA11a]
GO:0004519 - endonuclease activity [UniProtGOA11a]
GO:0016787 - hydrolase activity [UniProtGOA11a]
|MultiFun Terms:||cell processes → protection → cell killing|
|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]|
Enzymatic reaction of: RNase (toxin of the YafQ-DinJ toxin-antitoxin system)
EC Number: 3.1.26.-
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 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].
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 [Kim09]. A dinJ-yafQ deletion mutant is impaired in biofilm formation [KolodkinGal09a].
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].
|Molecular Function:||GO:0043565 - sequence-specific DNA binding [Prysak09]|
DNA binding site length: 16 base-pairs
Symmetry: Inverted Repeat
Consensus DNA Binding Sequence: CTGnATAnnTATnCAG
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
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
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
Kim09: 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
KolodkinGal09a: 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
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
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
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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