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    rapA RNA polymerase-binding ATPase and RNAP recycling factor [ Escherichia coli str. K-12 substr. MG1655 ]

    Gene ID: 948523, updated on 3-Dec-2024

    Summary

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    Official Symbol
    rapA
    Official Full Name
    RNA polymerase-binding ATPase and RNAP recycling factor
    Primary source
    ECOCYC:EG11083
    Locus tag
    b0059
    See related
    ASAP:ABE-0000198
    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
    ECK0060; hepA; yabA
    Summary
    HepA has sequence similarity to SWI2/SNF2 helicases. hepA is downstream of polB, but is not under lexA control. [More information is available at EcoGene: EG11083]. HepA causes increased recycling of RNA Polymerase and activates transcription under conditions under which the DNA is expected to be tightly supercoiled . [More information is available at EcoCyc: EG11083].
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    Genomic context

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    Sequence:
    NC_000913.3 (60358..63264, complement)

    NC_000913.3Genomic Context describing neighboring genes Neighboring gene putative uncharacterized protein YabP Neighboring gene protein YabQ Neighboring gene 23S rRNA pseudouridine(746) and tRNA pseudouridine(32) synthase Neighboring gene DNA polymerase II Neighboring gene L-ribulose-5-phosphate 4-epimerase AraD

    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. Structural basis of RNA polymerase recycling by the Swi2/Snf2 family of ATPase RapA in Escherichia coli. Qayyum MZ, et al. J Biol Chem, 2021 Dec. PMID 34774797, Free PMC Article
    2. Structural basis for activation of Swi2/Snf2 ATPase RapA by RNA polymerase. Shi W, et al. Nucleic Acids Res, 2021 Oct 11. PMID 34428297, Free PMC Article
    3. On the stability of stalled RNA polymerase and its removal by RapA. Portman JR, et al. Nucleic Acids Res, 2022 Jul 22. PMID 35819188, Free PMC Article
    4. Structure and function of RapA: a bacterial Swi2/Snf2 protein required for RNA polymerase recycling in transcription. Jin DJ, et al. Biochim Biophys Acta, 2011 Sep. PMID 21419241, Free PMC Article
    5. Chlorambucil-induced high mutation rate and suicidal gene downregulation in a base excision repair-deficient Escherichia coli strain. Salmelin C, et al. Mutat Res, 2002 Mar 20. PMID 11890942

    See all (30) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. On the stability of stalled RNA polymerase and its removal by RapA.
      Title: On the stability of stalled RNA polymerase and its removal by RapA.
    2. Structural basis of RNA polymerase recycling by the Swi2/Snf2 family of ATPase RapA in Escherichia coli.
      Title: Structural basis of RNA polymerase recycling by the Swi2/Snf2 family of ATPase RapA in Escherichia coli.
    3. Structural basis for activation of Swi2/Snf2 ATPase RapA by RNA polymerase.
      Title: Structural basis for activation of Swi2/Snf2 ATPase RapA by RNA polymerase.
    4. biochemical properties of RapA and role in RNAP recycling during transcription [review]
      Title: Structure and function of RapA: a bacterial Swi2/Snf2 protein required for RNA polymerase recycling in transcription.
    5. Mutations in the interface between RapA's SWI/SNF family chromatin remodeling complex and double-stranded nucleic acid-binding domains significantly alter adenosine triphosphate (ATP) hydrolysis in purified RapA.
      Title: RapA, the SWI/SNF subunit of Escherichia coli RNA polymerase, promotes the release of nascent RNA from transcription complexes.
    6. RapA binds and remodels RNA during transcription.
      Title: Escherichia coli RNA polymerase-associated SWI/SNF protein RapA: evidence for RNA-directed binding and remodeling activity.
    7. A comparison of the biofilm matrix of the wild-type and rapA strains revealed decreased polysaccharide quantities and coverage in the mutant biofilms
      Title: Role of the rapA gene in controlling antibiotic resistance of Escherichia coli biofilms.
    8. N-terminus verified by Edman degradation on mature peptide
      Title: RapA, a bacterial homolog of SWI2/SNF2, stimulates RNA polymerase recycling in transcription.
    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 ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP hydrolysis activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables bacterial-type RNA polymerase core enzyme binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables hydrolase activity, acting on acid anhydrides IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleic acid binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables nucleosome array spacer activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in heterochromatin formation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    RNA polymerase-binding ATPase and RNAP recycling factor

    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
      60358..63264 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NP_414601.1 RNA polymerase-binding ATPase and RNAP recycling factor [Escherichia coli str. K-12 substr. MG1655]

      See identical proteins and their annotated locations for NP_414601.1

      Status: PROVISIONAL

      UniProtKB/TrEMBL
      A0A376FQ46, A0AAD2UAC7
      Conserved Domains (1) summary
      PRK04914
      Location:2 → 966
      PRK04914; RNA polymerase-associated protein RapA
    Nucleotide Protein
    Heading Accession and Version

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    Other Literature Sources
    Molecular Biology Databases
    Research Materials