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MetaCyc Protein: YefM-YoeB antitoxin/toxin complex and DNA-binding transcriptional repressor
Inferred from experiment

Synonyms: YefMB

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of YefM-YoeB antitoxin/toxin complex and DNA-binding transcriptional repressor = [YoeB][YefM]2
         toxin of the YoeB-YefM toxin-antitoxin pair = YoeB (extended summary available)
         YefM antitoxin of the YoeB-YefM toxin-antitoxin pair and DNA binding transcriptional repressor = YefM

YefM is a transcriptional DNA-binding autorepressor for the yefM-yoeB operon. In addition, YefM also functions as an antitoxin to form a complex with YoeB, which is a toxin that is counteracted by YefM antitoxin [Kedzierska07]. YefM can bind alone with low affinity to the yefM-yoeB operator, but together with YoeB it has an enhanced DNA-binding affinity compared to free YefM [Kedzierska07]. YoeB enhances the interaction with YefM by affecting the YefM conformation to one that is more favorable for DNA binding and/or by stabilizing the nucleoprotein complex at the operator site and reducing basal expression of the yefM-yoeB operon [Kedzierska07, Bailey09].

The yefM gene is upregulated during growth in biofilms [Ren04] and yefM-yoeB is upregulated in persister cells [Shah06]; it is probable that derepression of yefM-yoeB autoregulation occurs in these circumstances in response to an as-yet-unknown environmental or cell cycle signal(s) that interferes with the YefM-YoeB-operator interaction [Bailey09].

The operator site 5' of yefM-yoeB comprises adjacent long (L) and short (S) palindromes with core 5'-TGTACA-3' motifs with a center-to-center distance of 12 bp [Kedzierska07], which was suggested to be crucial for the correct stable positioning of YefM-YoeB at the two repeats [Bailey09]. This sequence organization is common in yefM-yoeB regulatory regions in diverse genomes, suggesting that interaction of YefM-YoeB with these motifs is a conserved mechanism of operon autoregulation [Kedzierska07].

Nevertheless, YefM originally was described as a native unstructured protein [Cherny04]; later it was reevaluated as experimental, and modeling data have demonstrated that the protein is at least partially folded [Kedzierska07, Pomerantsev01] and dimeric [Kedzierska07].

The YefM antitoxin forms a heterotrimeric complex with the YoeB toxin (YefM2-YoeB) [Cherny05, Kamada05]. The tertiary structure of the YoeB toxin and the YefM2-YoeB complex has been described [Kamada05]. In the complex, one C terminus in the YefM homodimer is unfolded and the other one shows an α-helical conformation and conceals the endoribonuclease fold of YoeB. Two N-terminal segments of YefM form a symmetrical dimer within the YefM2-YoeB heterotrimeric complex and do not contact YoeB directly [Bailey09].

YefM does not possess a canonical DNA-binding motif, but instead a pair of basic residues, R10 and R31, conserved in many YefM homologs are absolutely necessary for DNA binding by the YefM-YoeB complex [Grady03, Bailey09, Kamada05].

Molecular Weight: 30.0 kD (experimental) [Kamada05]

Gene-Reaction Schematic

Gene-Reaction Schematic

Created in EcoCyc 10-Jan-2009 by Santos-Zavaleta A, UNAM
Imported from EcoCyc 30-Sep-2015 by Paley S, SRI International

DNA binding site length: 14 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: TCATTGTACAATGA

Component enzyme of YefM-YoeB antitoxin/toxin complex and DNA-binding transcriptional repressor : toxin of the YoeB-YefM toxin-antitoxin pair

Synonyms: YoeB

Gene: yoeB Accession Numbers: G0-9121 (MetaCyc), b4539, ECK2011

Locations: cytosol

Sequence Length: 84 AAs

Molecular Weight: 10.216 kD (from nucleotide sequence)

GO Terms:
Biological Process:
Inferred from experimentGO:0006402 - mRNA catabolic process [ChristensenDals08]
Inferred from experimentGO:0044010 - single-species biofilm formation [Kim09a]
Inferred from experimentGO:0045947 - negative regulation of translational initiation [Zhang09b]
Inferred from experimentGO:0090502 - RNA phosphodiester bond hydrolysis, endonucleolytic [Feng13, Kamada05]
Inferred from experimentGO:0098795 - mRNA cleavage involved in gene silencing [Christensen04]
Inferred from experimentGO:1903507 - negative regulation of nucleic acid-templated transcription [Kedzierska07]
Inferred by computational analysisGO:0006351 - transcription, DNA-templated [UniProtGOA11a]
Inferred by computational analysisGO:0006355 - regulation of transcription, DNA-templated [UniProtGOA11a]
Inferred by computational analysisGO:0006401 - RNA catabolic process [GOA01a]
Molecular Function:
Inferred from experimentGO:0003714 - transcription corepressor activity [Kedzierska07]
Inferred from experimentGO:0004521 - endoribonuclease activity [Kamada05]
Inferred from experimentGO:0005515 - protein binding [Cherny05]
Inferred from experimentGO:0016892 - endoribonuclease activity, producing 3'-phosphomonoesters [Feng13]
Inferred from experimentGO:0043024 - ribosomal small subunit binding [Zhang09b]
Inferred by computational analysisGO:0003723 - RNA binding [UniProtGOA11a]
Inferred by computational analysisGO:0004518 - nuclease activity [UniProtGOA11a]
Inferred by computational analysisGO:0004519 - endonuclease activity [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0016787 - hydrolase activity [UniProtGOA11a]
Cellular Component:
Inferred by computational analysisGO:0005829 - cytosol [DiazMejia09]

MultiFun Terms: cell processesdefense/survival

Unification Links: EcoliWiki:b4539, Protein Model Portal:P69348, RefSeq:YP_588458, SMR:P69348, UniProt:P69348

Relationship Links: InterPro:IN-FAMILY:IPR009614, PDB:Structure:2A6Q, PDB:Structure:2A6R, PDB:Structure:2A6S, Pfam:IN-FAMILY:PF06769

an mRNA + H2O → an RNase product with a 3' phosphate + an RNase product with a 5' OH

YoeB is the toxin of the YoeB-YefM toxin-antitoxin pair [Grady03, Cherny04]. The YoeB toxin induces cleavage of translated mRNAs. YoeB can be activated by overproduction of the Lon protease (which is lethal), suggesting that Lon degrades YefM [Christensen04]. YoeB inhibits translation initiation by interacting with the A site of the ribosome [Zhang09b], leading to mRNA cleavage after the second position in the A-site codon and producing a 3'-phosphate product [Feng13].

Earlier experiments showed that YoeB is an endoribonuclease that preferentially cleaves at the 3' end of purine ribonucleotides [Kamada05]. The activity is dependent on mRNA translation in vivo, and the cleavage pattern is determined by the reading frame [ChristensenDals08].

YoeB recognizes and binds to an unstructured peptide sequence within YefM [Cherny04]. The YoeB-YefM complex was initially reported to have a stoichiometry of YoeB2-YefM1 [Cherny05]. However, crystal structures show a YoeB1-YefM2 complex where interaction with YefM induces a conformational change in the YoeB RNase catalytic site [Kamada05]. YoeB enhances the transcription repressor activity of YefM [Kedzierska07].

A crystal structure of YoeB bound to a 70S ribosome has been solved. A YoeB dimer was found to bind to the ribosomal A site [Feng13].

yefM-yoeB is overexpressed in a selected cell population that resembles persister cells [Shah06]. Deletion of yoeB increases biofilm formation [Kim09a]. Overexpression of YoeB causes loss of cell viability approximately 2 hours after induction [KolodkinGal09].

Review: [Yamaguchi11]

Citations: [Tsilibaris07, Kawano09, Winther09, Leplae11, Maisonneuve11, Polom13]

Subunit of YefM-YoeB antitoxin/toxin complex and DNA-binding transcriptional repressor: YefM antitoxin of the YoeB-YefM toxin-antitoxin pair and DNA binding transcriptional repressor

Synonyms: YefM

Gene: yefM Accession Numbers: EG12844 (MetaCyc), b2017, ECK2012

Sequence Length: 83 AAs

Molecular Weight: 9.308 kD (from nucleotide sequence)

GO Terms:
Biological Process:
Inferred from experimentGO:0044010 - single-species biofilm formation [Kim09a]
Inferred from experimentGO:0045892 - negative regulation of transcription, DNA-templated [Kedzierska07]
Inferred by computational analysisGO:0006351 - transcription, DNA-templated [UniProtGOA11a]
Inferred by computational analysisGO:0006355 - regulation of transcription, DNA-templated [UniProtGOA11a]
Molecular Function:
Inferred from experimentGO:0015643 - toxic substance binding [Cherny05]
Inferred from experimentGO:0042803 - protein homodimerization activity [Kedzierska07]
Inferred from experimentGO:0043565 - sequence-specific DNA binding [Kedzierska07]
Inferred by computational analysisGO:0003677 - DNA binding [UniProtGOA11a]

MultiFun Terms: cell processesdefense/survival

Unification Links: EcoliWiki:b2017, Pride:P69346, Protein Model Portal:P69346, RefSeq:NP_416521, SMR:P69346, UniProt:P69346

Relationship Links: InterPro:IN-FAMILY:IPR006442, PDB:Structure:2A6Q, Pfam:IN-FAMILY:PF02604


Bailey09: Bailey SE, Hayes F (2009). "Influence of operator site geometry on transcriptional control by the YefM-YoeB toxin-antitoxin complex." J Bacteriol 191(3);762-72. PMID: 19028895

Cherny04: Cherny I, Gazit E (2004). "The YefM antitoxin defines a family of natively unfolded proteins: implications as a novel antibacterial target." J Biol Chem 279(9);8252-61. PMID: 14672926

Cherny05: Cherny I, Rockah L, Gazit E (2005). "The YoeB toxin is a folded protein that forms a physical complex with the unfolded YefM antitoxin. Implications for a structural-based differential stability of toxin-antitoxin systems." J Biol Chem 280(34);30063-72. PMID: 15980067

Christensen04: Christensen SK, Maenhaut-Michel G, Mine N, Gottesman S, Gerdes K, Van Melderen L (2004). "Overproduction of the Lon protease triggers inhibition of translation in Escherichia coli: involvement of the yefM-yoeB toxin-antitoxin system." Mol Microbiol 51(6);1705-17. PMID: 15009896

ChristensenDals08: Christensen-Dalsgaard M, Gerdes K (2008). "Translation affects YoeB and MazF messenger RNA interferase activities by different mechanisms." Nucleic Acids Res 36(20);6472-81. PMID: 18854355

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

Feng13: Feng S, Chen Y, Kamada K, Wang H, Tang K, Wang M, Gao YG (2013). "YoeB-ribosome structure: a canonical RNase that requires the ribosome for its specific activity." Nucleic Acids Res 41(20);9549-56. PMID: 23945936

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

Grady03: Grady R, Hayes F (2003). "Axe-Txe, a broad-spectrum proteic toxin-antitoxin system specified by a multidrug-resistant, clinical isolate of Enterococcus faecium." Mol Microbiol 47(5);1419-32. PMID: 12603745

Kamada05: Kamada K, Hanaoka F (2005). "Conformational change in the catalytic site of the ribonuclease YoeB toxin by YefM antitoxin." Mol Cell 19(4);497-509. PMID: 16109374

Kawano09: Kawano H, Hirokawa Y, Mori H (2009). "Long-term survival of Escherichia coli lacking the HipBA toxin-antitoxin system during prolonged cultivation." Biosci Biotechnol Biochem 73(1);117-23. PMID: 19129642

Kedzierska07: Kedzierska B, Lian LY, Hayes F (2007). "Toxin-antitoxin regulation: bimodal interaction of YefM-YoeB with paired DNA palindromes exerts transcriptional autorepression." Nucleic Acids Res 35(1);325-39. PMID: 17170003

Kim09a: 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

Leplae11: Leplae R, Geeraerts D, Hallez R, Guglielmini J, Dreze P, Van Melderen L (2011). "Diversity of bacterial type II toxin-antitoxin systems: a comprehensive search and functional analysis of novel families." Nucleic Acids Res 39(13);5513-25. PMID: 21422074

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

Polom13: Polom D, Boss L, Węgrzyn G, Hayes F, Kędzierska B (2013). "Amino acid residues crucial for specificity of toxin-antitoxin interactions in the homologous Axe-Txe and YefM-YoeB complexes." FEBS J 280(22);5906-18. PMID: 24028219

Pomerantsev01: Pomerantsev AP, Golovliov IR, Ohara Y, Mokrievich AN, Obuchi M, Norqvist A, Kuoppa K, Pavlov VM (2001). "Genetic organization of the Francisella plasmid pFNL10." Plasmid 46(3);210-22. PMID: 11735370

Ren04: Ren D, Bedzyk LA, Thomas SM, Ye RW, Wood TK (2004). "Gene expression in Escherichia coli biofilms." Appl Microbiol Biotechnol 64(4);515-24. PMID: 14727089

Shah06: Shah D, Zhang Z, Khodursky A, Kaldalu N, Kurg K, Lewis K (2006). "Persisters: a distinct physiological state of E. coli." BMC Microbiol 6;53. PMID: 16768798

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

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

Winther09: Winther KS, Gerdes K (2009). "Ectopic production of VapCs from Enterobacteria inhibits translation and trans-activates YoeB mRNA interferase." Mol Microbiol 72(4);918-30. PMID: 19400780

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, Inouye M (2009). "The inhibitory mechanism of protein synthesis by YoeB, an Escherichia coli toxin." J Biol Chem 284(11);6627-38. PMID: 19124462

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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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