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

    Gene ID: 944911, updated on 3-Dec-2024

    Summary

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    Official Symbol
    yafQ
    Official Full Name
    ribosome-dependent mRNA interferase toxin YafQ
    Primary source
    ECOCYC:G6109
    Locus tag
    b0225
    See related
    ASAP:ABE-0000761
    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
    ECK0226
    Summary
    YafQ is homologous to the RelE toxin, which inhibits translation as a sequence-specific mRNA endoribonuclease. [More information is available at EcoGene: EG13154]. The YafQ-DinJ toxin-antitoxin system was identified by its similarity to the RelE-RelB toxin-antitoxin system . [More information is available at EcoCyc: G6109].
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    Genomic context

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    Sequence:
    NC_000913.3 (245961..246239, complement)

    NC_000913.3Genomic Context describing neighboring genes Neighboring gene D-sedoheptulose 7-phosphate isomerase Neighboring gene putative glutamine amidotransferase YafJ Neighboring gene peptidoglycan meso-diaminopimelic acid protein amidase A Neighboring gene antitoxin/DNA-binding transcriptional repressor DinJ Neighboring gene NlpC/P60 family protein YafL

    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. Toxin YafQ increases persister cell formation by reducing indole signalling. Hu Y, et al. Environ Microbiol, 2015 Apr. PMID 25041421
    2. The chromosomal toxin gene yafQ is a determinant of multidrug tolerance for Escherichia coli growing in a biofilm. Harrison JJ, et al. Antimicrob Agents Chemother, 2009 Jun. PMID 19307375, Free PMC Article
    3. Molecular basis of ribosome recognition and mRNA hydrolysis by the E. coli YafQ toxin. Maehigashi T, et al. Nucleic Acids Res, 2015 Sep 18. PMID 26261214, Free PMC Article
    4. Mechanisms of toxin inhibition and transcriptional repression by Escherichia coli DinJ-YafQ. Ruangprasert A, et al. J Biol Chem, 2014 Jul 25. PMID 24898247, Free PMC Article
    5. Characterization of Escherichia coli dinJ-yafQ toxin-antitoxin system using insights from mutagenesis data. Armalyte J, et al. J Bacteriol, 2012 Mar. PMID 22247505, Free PMC Article

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The findings demonstrate the plasticity of ribosome-dependent toxin active site residues by the E. coli YafQ toxin and further our understanding of which toxin residues are important for function.
      Title: Molecular basis of ribosome recognition and mRNA hydrolysis by the E. coli YafQ toxin.
    2. YafQ increases persistence by reducing indole, and toxin/antitoxin systems are related to cell signalling.
      Title: Toxin YafQ increases persister cell formation by reducing indole signalling.
    3. The endoribonuclease activity of YafQ was inhibited in the complex with DinJ antitoxin in vitro.
      Title: Characterization of Escherichia coli dinJ-yafQ toxin-antitoxin system using insights from mutagenesis data.
    4. YafQ endoribonuclease expression resulted in translation, but not transcription or replication defects.
      Title: Bacterial toxin YafQ is an endoribonuclease that associates with the ribosome and blocks translation elongation through sequence-specific and frame-dependent mRNA cleavage.
    5. Acts as toxin in active toxin-antitoxin module with DinJ. Structure modelling suggests that it might act as a sequence-specific mRNA endoribonuclease.
      Title: Escherichia coli dinJ-yafQ genes act as a toxin-antitoxin module.
    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 DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA endonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ribosome binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in mRNA catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within mRNA catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of growth NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    acts_upstream_of_or_within response to antibiotic IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in single-species biofilm formation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within single-species biofilm formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in translational termination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within translational termination IDA
    Inferred from Direct Assay
    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 YafQ

    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
      245961..246239 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NP_414760.1 ribosome-dependent mRNA interferase toxin YafQ [Escherichia coli str. K-12 substr. MG1655]

      See identical proteins and their annotated locations for NP_414760.1

      Status: PROVISIONAL

      UniProtKB/TrEMBL
      A0A8S7RG15, A0A8T6A7D3
      Conserved Domains (1) summary
      COG3041
      Location:3 → 91
      YafQ; mRNA-degrading endonuclease (mRNA interferase) YafQ, toxin component of the YafQ-DinJ toxin-antitoxin module [Translation, ribosomal structure and biogenesis]
    Nucleotide Protein
    Heading Accession and Version

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