yoeB [Escherichia coli str. K-12 substr. MG1655] - Gene

Summary

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Official Symbol: yoeB
Primary source: ECOCYC:G0-9121
Locus tag: b4539
See related: ASAP:ABE-0285060
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Escherichia coli str. K-12 substr. MG1655 (strain: K-12, substrain: MG1655)
Lineage: Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia
Also known as: ECK2011
Summary: YefM-YoeB is the only toxin/antoxin pair involved in Lon dependent lethality. [More information is available at EcoGene: EG14356]. YoeB and YefM are a toxin-antitoxin pair . [More information is available at EcoCyc: G0-9121].
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Genomic context

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Sequence:: NC_000913.3 (2089211..2089465, complement)

NC_000913.3 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_000913.3

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

the stability of monomeric YoeB is reduced approximately 20 degrees C, consistent with potential YoeB activation during heat shock in E. coli as previously demonstrated. These data provide a molecular basis for the ability of YoeB to function in response to thermal stress
Title: Monomeric YoeB toxin retains RNase activity but adopts an obligate dimeric form for thermal stability.
The authors propose that heat-activated YoeB may serve a quality control function, facilitating the recycling of stalled translation complexes through ribosome rescue pathways.
Title: YoeB toxin is activated during thermal stress.
Based on molecular modeling, selected amino acid residues were changed to assess which positions were crucial in the specificity of toxin-antitoxin interaction in the related Axe-Txe and YefM-YoeB complexes.
Title: Amino acid residues crucial for specificity of toxin-antitoxin interactions in the homologous Axe-Txe and YefM-YoeB complexes.
VapC overproduction leads to Lon-dependent trans-activation of YoeB, in a way that leads to preferential YoeB-mediated cleavage at mRNA stop-codons.
Title: Ectopic production of VapCs from Enterobacteria inhibits translation and trans-activates YoeB mRNA interferase.
YoeB corepressor greatly enhances the YefM-operator interaction.
Title: Influence of operator site geometry on transcriptional control by the YefM-YoeB toxin-antitoxin complex.
Model mRNAs carrying frameshift mutations exhibited a YoeB-mediated cleavage pattern consistent with the reading frameshift thus giving strong evidence that YoeB cleavage specificity was determined by the translational reading frame.
Title: Translation affects YoeB and MazF messenger RNA interferase activities by different mechanisms.
The effect of yefM and yoeB from Streptococcus pneumoniae (S. pneumoniae) on E. coli, and the interaction of the proteins from E. coli with the S. pneumoniae proteins are reported.
Title: The yefM-yoeB toxin-antitoxin systems of Escherichia coli and Streptococcus pneumoniae: functional and structural correlation.
YoeB acts as a repression enhancer of the yefM-yoeB cassette.
Title: Toxin-antitoxin regulation: bimodal interaction of YefM-YoeB with paired DNA palindromes exerts transcriptional autorepression.
Interaction of YefM with YoeB in the YefM2/YoeB heterotrimer induces conformational changes in the RNase catalytic site of YoeB, an enzyme that preferentially cleaves at the 3' end of purine ribonucleotides
Title: Conformational change in the catalytic site of the ribonuclease YoeB toxin by YefM antitoxin.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by EcoCyc

Function	Evidence Code	Pubs
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA endonuclease activity	IDA Inferred from Direct Assay more info	PubMed
enables RNA endonuclease activity, producing 3'-phosphomonoesters	IDA Inferred from Direct Assay more info	PubMed
enables endonuclease activity	IBA Inferred from Biological aspect of Ancestor more info
enables endonuclease activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables ribosomal small subunit binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA catabolic process	IEA Inferred from Electronic Annotation more info
involved_in global gene silencing by mRNA cleavage	IBA Inferred from Biological aspect of Ancestor more info
involved_in global gene silencing by mRNA cleavage	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within mRNA catabolic process	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of translational initiation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of DNA-templated transcription	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of growth	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of_or_within response to heat	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within response to heat	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within single-species biofilm formation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of toxin-antitoxin complex	IPI Inferred from Physical Interaction more info	PubMed

General protein information

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Preferred Names: ribosome-dependent mRNA interferase toxin YoeB

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_000913.3 Reference assembly

Range

2089211..2089465 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

YP_588458.1 ribosome-dependent mRNA interferase toxin YoeB [Escherichia coli str. K-12 substr. MG1655]

See identical proteins and their annotated locations for YP_588458.1

Status: PROVISIONAL

UniProtKB/TrEMBL

A0A376ZFU4

Conserved Domains (1) summary

pfam06769
Location:5 → 84

YoeB_toxin; YoeB-like toxin of bacterial type II toxin-antitoxin system