Escherichia coli K-12 substr. MG1655 Enzyme: ribosome-dependent mRNA interferase, toxin of the YafO-YafN toxin-antitoxin system

Gene: yafO Accession Numbers: G6117 (EcoCyc), b0233, ECK0234

Regulation Summary Diagram: ?

Regulation summary diagram for yafO

YafO is the toxin of the YafO-YafN toxin-antitoxin system, acting as a ribosome-dependent mRNA interferase. When it is associated with the ribosome, YafO inhibits protein synthesis by cleaving mRNAs downstream of the translation initiation site [Zhang09b, ChristensenDals10]. YafO alone does not have endoribonuclease activity [Zhang09b].

Ectopic expression of yafO causes inhibition of cell growth [Brown03, Zhang09b, ChristensenDals10].

Expression of yafO is increased by UV irradiation [Courcelle01]; the dinB promoter is SOS-regulated [ChristensenDals10]. The promoter upstream of yafN appears to be autorepressed by YafN [ChristensenDals10].

Polar dinB mutations affecting the dinB-yafNOP operon reduce spontaneous mutagenesis [McKenzie03]; however, only DinB is required for stress-induced mutagenesis [Singletary09].

Review: [Yamaguchi11]

Locations: cytosol

Map Position: [252,301 -> 252,699] (5.44 centisomes, 20°)
Length: 399 bp / 132 aa

Molecular Weight of Polypeptide: 15.488 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0000795 , EchoBASE:EB2946 , EcoGene:EG13152 , EcoliWiki:b0233 , OU-Microarray:b0233 , PortEco:yafO , Protein Model Portal:Q47157 , RefSeq:NP_414768 , RegulonDB:G6117 , String:511145.b0233 , UniProt:Q47157

Relationship Links: InterPro:IN-FAMILY:IPR020353 , Pfam:IN-FAMILY:PF13957 , ProDom:IN-FAMILY:PD082093

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for yafO

GO Terms:

Biological Process: GO:0017148 - negative regulation of translation Inferred from experiment [Zhang09b]
GO:0090502 - RNA phosphodiester bond hydrolysis, endonucleolytic Inferred from experiment [ChristensenDals10]
GO:0006281 - DNA repair Inferred by computational analysis [UniProtGOA11]
GO:0006974 - cellular response to DNA damage stimulus Inferred by computational analysis [UniProtGOA11]
GO:0009432 - SOS response 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 [ChristensenDals10]
GO:0043023 - ribosomal large subunit binding Inferred from experiment [Zhang09b]
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]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell processes protection cell killing
regulation type of regulation posttranscriptional translation attenuation and efficiency

Essentiality data for yafO 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 ? 09-Dec-2009 by Keseler I , SRI International

Enzymatic reaction of: ribosome-dependent mRNA interferase

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.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

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

Brown03: Brown JM, Shaw KJ (2003). "A novel family of Escherichia coli toxin-antitoxin gene pairs." J Bacteriol 185(22);6600-8. PMID: 14594833

ChristensenDals10: Christensen-Dalsgaard M, Jorgensen MG, Gerdes K (2010). "Three new RelE-homologous mRNA interferases of Escherichia coli differentially induced by environmental stresses." Mol Microbiol 75(2):333-48. PMID: 19943910

Courcelle01: Courcelle J, Khodursky A, Peter B, Brown PO, Hanawalt PC (2001). "Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli." Genetics 158(1);41-64. PMID: 11333217

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

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

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

McKenzie03: McKenzie GJ, Magner DB, Lee PL, Rosenberg SM (2003). "The dinB operon and spontaneous mutation in Escherichia coli." J Bacteriol 185(13);3972-7. PMID: 12813093

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

Singletary09: Singletary LA, Gibson JL, Tanner EJ, McKenzie GJ, Lee PL, Gonzalez C, Rosenberg SM (2009). "An SOS-regulated type 2 toxin-antitoxin system." J Bacteriol 191(24);7456-65. PMID: 19837801

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

Zhang09b: Zhang Y, Yamaguchi Y, Inouye M (2009). "Characterization of YafO, an Escherichia coli Toxin." J Biol Chem 284(38);25522-31. PMID: 19617347

Other References Related to Gene Regulation

BuryMone09: Bury-Mone S, Nomane Y, Reymond N, Barbet R, Jacquet E, Imbeaud S, Jacq A, Bouloc P (2009). "Global analysis of extracytoplasmic stress signaling in Escherichia coli." PLoS Genet 5(9);e1000651. PMID: 19763168

Fernandez00: Fernandez De Henestrosa AR, Ogi T, Aoyagi S, Chafin D, Hayes JJ, Ohmori H, Woodgate R (2000). "Identification of additional genes belonging to the LexA regulon in Escherichia coli." Mol Microbiol 35(6);1560-72. PMID: 10760155

Gillor08: Gillor O, Vriezen JA, Riley MA (2008). "The role of SOS boxes in enteric bacteriocin regulation." Microbiology 154(Pt 6);1783-92. PMID: 18524933

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

Kaleta10: Kaleta C, Gohler A, Schuster S, Jahreis K, Guthke R, Nikolajewa S (2010). "Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis." BMC Syst Biol 4;116. PMID: 20718955

Ohmori95: Ohmori H, Hatada E, Qiao Y, Tsuji M, Fukuda R (1995). "dinP, a new gene in Escherichia coli, whose product shows similarities to UmuC and its homologues." Mutat Res 347(1);1-7. PMID: 7596361

Wade05: Wade JT, Reppas NB, Church GM, Struhl K (2005). "Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites." Genes Dev 19(21);2619-30. PMID: 16264194

Zaslaver06: Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette MG, Alon U (2006). "A comprehensive library of fluorescent transcriptional reporters for Escherichia coli." Nat Methods 3(8);623-8. PMID: 16862137

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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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