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

    Gene ID: 1450274, updated on 3-Dec-2024

    Summary

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    Official Symbol
    yoeB
    Official Full Name
    ribosome-dependent mRNA interferase toxin 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_000913.3Genomic Context describing neighboring genes Neighboring gene putative DNA-binding transcriptional regulator YeeY Neighboring gene putative epimerase YeeZ Neighboring gene YefM antitoxin of the YoeB-YefM toxin-antitoxin pair and DNA binding transcriptional repressor Neighboring gene his operon leader peptide Neighboring gene ATP phosphoribosyltransferase

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_000913.3

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. YoeB toxin is activated during thermal stress. Janssen BD, et al. Microbiologyopen, 2015 Aug. PMID 26147890, Free PMC Article
    2. YoeB-ribosome structure: a canonical RNase that requires the ribosome for its specific activity. Feng S, et al. Nucleic Acids Res, 2013 Nov. PMID 23945936, Free PMC Article
    3. Monomeric YoeB toxin retains RNase activity but adopts an obligate dimeric form for thermal stability. Pavelich IJ, et al. Nucleic Acids Res, 2019 Nov 4. PMID 31501867, Free PMC Article
    4. The yefM-yoeB toxin-antitoxin systems of Escherichia coli and Streptococcus pneumoniae: functional and structural correlation. Nieto C, et al. J Bacteriol, 2007 Feb. PMID 17071753, Free PMC Article
    5. Genetic organization of the Francisella plasmid pFNL10. Pomerantsev AP, et al. Plasmid, 2001 Nov. PMID 11735370

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    2. 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.
    3. 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.
    4. 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.
    5. YoeB corepressor greatly enhances the YefM-operator interaction.
      Title: Influence of operator site geometry on transcriptional control by the YefM-YoeB toxin-antitoxin complex.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    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

    1. NC_000913.3 Reference assembly

      Range
      2089211..2089465 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. 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
    Nucleotide Protein
    Heading Accession and Version

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