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    arfA alternative ribosome-rescue factor A [ Escherichia coli str. K-12 substr. MG1655 ]

    Gene ID: 1450289, updated on 3-Dec-2024

    Summary

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    Official Symbol
    arfA
    Official Full Name
    alternative ribosome-rescue factor A
    Primary source
    ECOCYC:G0-10465
    Locus tag
    b4550
    See related
    ASAP:ABE-0285071
    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
    ECK3278; yhdL
    Summary
    yhdL RNA has been detected during efforts to identify noncoding RNAs; however, the length of the RNA detected appears to be too short to encode the entire predicted 72 residue polypeptide . [More information is available at EcoCyc: G0-10465].
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    Genomic context

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    Sequence:
    NC_000913.3 (3438431..3438649, complement)

    NC_000913.3Genomic Context describing neighboring genes Neighboring gene 16S rRNA m(5)C967 methyltransferase Neighboring gene NAD-binding component of Trk potassium transporters Neighboring gene large conductance mechanosensitive channel Neighboring gene DNA-binding transcriptional activator ZntR Neighboring gene DUF1992 domain-containing protein YhdN

    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. Translational termination without a stop codon. James NR, et al. Science, 2016 Dec 16. PMID 27934701, Free PMC Article
    2. Molecular determinants of release factor 2 for ArfA-mediated ribosome rescue. Kurita D, et al. J Biol Chem, 2020 Sep 18. PMID 32727848, Free PMC Article
    3. Translation Stress Positively Regulates MscL-Dependent Excretion of Cytoplasmic Proteins. Morra R, et al. mBio, 2018 Jan 30. PMID 29382730, Free PMC Article
    4. Mechanism of ribosome rescue by ArfA and RF2. Demo G, et al. Elife, 2017 Mar 16. PMID 28300532, Free PMC Article
    5. A merR homologue at 74 minutes on the Escherichia coli genome. Christie GE, et al. Gene, 1994 Aug 19. PMID 8063098

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Molecular determinants of release factor 2 for ArfA-mediated ribosome rescue.
      Title: Molecular determinants of release factor 2 for ArfA-mediated ribosome rescue.
    2. Collectively, the findings indicate that MscL-dependent protein excretion is positively regulated in response to both osmotic stress and arfA-mediated translational stress.
      Title: Translation Stress Positively Regulates MscL-Dependent Excretion of Cytoplasmic Proteins.
    3. The structures demonstrate how ArfA 'senses' the vacant mRNA tunnel and activates RF2 to mediate peptide release without a stop codon, allowing stalled ribosomes to be recycled.
      Title: Mechanism of ribosome rescue by ArfA and RF2.
    4. ArfA binds within the ribosomal mRNA channel and substitutes for the absent stop codon in the A site by specifically recruiting release factor 2 (RF2), initially in a compact preaccommodated state.
      Title: Translational termination without a stop codon.
    5. This study demonstrated the sites and modes of binding of ArfA to the stalled ribosome.
      Title: ArfA recognizes the lack of mRNA in the mRNA channel after RF2 binding for ribosome rescue.
    6. The authors characterized the ArfA pathway of non-productive translation complexe resolution in vitro and identified RF2 as a factor that cooperates with ArfA to hydrolyse peptidyl-tRNAs located in the P-site of the stalled ribosome.
      Title: ArfA recruits release factor 2 to rescue stalled ribosomes by peptidyl-tRNA hydrolysis in Escherichia coli.
    7. ArfA recruits RF2 into the A site of the ribosome to facilitate peptidyl-tRNA hydrolysis.
      Title: ArfA recruits RF2 into stalled ribosomes.
    8. tmRNA (ssrA) regulates the synthesis of ArfA.
      Title: tmRNA regulates synthesis of the ArfA ribosome rescue factor.
    9. These results indicate that ArfA (YhdL) rescues the ribosome stalled at the 3' end of a non-stop mRNA without involving trans-translation.
      Title: Ribosome rescue by Escherichia coli ArfA (YhdL) in the absence of trans-translation system.
    Submit: New GeneRIF Correction

    General gene information

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    Homology

    Gene Ontology Provided by EcoCyc

    Function Evidence Code Pubs
    enables rRNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ribosomal large subunit binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables tRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables tRNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in regulation of translation IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within rescue of stalled ribosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in rescue of stalled ribosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within rescue of stalled ribosome IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    alternative ribosome-rescue factor A

    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
      3438431..3438649 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. YP_588467.1 alternative ribosome-rescue factor A [Escherichia coli str. K-12 substr. MG1655]

      See identical proteins and their annotated locations for YP_588467.1

      Status: PROVISIONAL

      Conserved Domains (1) summary
      COG3036
      Location:3 → 63
      ArfA; Stalled ribosome alternative rescue factor ArfA [Translation, ribosomal structure and biogenesis]
    Nucleotide Protein
    Heading Accession and Version

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