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    rfaH transcription antiterminator RfaH [ Escherichia coli str. K-12 substr. MG1655 ]

    Gene ID: 948327, updated on 3-Dec-2024

    Summary

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    Official Symbol
    rfaH
    Official Full Name
    transcription antiterminator RfaH
    Primary source
    ECOCYC:EG10839
    Locus tag
    b3842
    See related
    ASAP:ABE-0012553
    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
    ECK3834; hlyT; sfrB
    Summary
    RfaH is recruited by JUMPstart/ops sequence elements. [More information is available at EcoGene: EG10839]. RfaH acts as a transcriptional antiterminator for a subset of operons required for the production of extracellular components such as lipopolysaccharide . [More information is available at EcoCyc: EG10839].
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    Genomic context

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    Sequence:
    NC_000913.3 (4024333..4024821, complement)

    NC_000913.3Genomic Context describing neighboring genes Neighboring gene twin arginine protein translocation system - TatB protein Neighboring gene twin arginine protein translocation system - TatC protein Neighboring gene 3' -> 5' ssDNA/RNA exonuclease TatD Neighboring gene 3-octaprenyl-4-hydroxybenzoate decarboxylase Neighboring gene NAD(P)H-flavin reductase

    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. RfaH and the ops element, components of a novel system controlling bacterial transcription elongation. Bailey MJ, et al. Mol Microbiol, 1997 Dec. PMID 9426123
    2. Crystallization and preliminary crystallographic analysis of the transcriptional regulator RfaH from Escherichia coli and its complex with ops DNA. Vassylyeva MN, et al. Acta Crystallogr Sect F Struct Biol Cryst Commun, 2006 Oct 1. PMID 17012804, Free PMC Article
    3. Transcriptional regulation through RfaH contributes to intestinal colonization by Escherichia coli. Nagy G, et al. FEMS Microbiol Lett, 2005 Mar 1. PMID 15727837
    4. RpoS and RpoN are involved in the growth-dependent regulation of rfaH transcription and O antigen expression in Salmonella enterica serovar Typhi. Bittner M, et al. Microb Pathog, 2004 Jan. PMID 14643636
    5. O-antigen expression in Salmonella enterica serovar Typhi is regulated by nitrogen availability through RpoN-mediated transcriptional control of the rfaH gene. Bittner M, et al. Microbiology (Reading), 2002 Dec. PMID 12480883

    See all (55) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. RfaH Counter-Silences Inhibition of Transcript Elongation by H-NS-StpA Nucleoprotein Filaments in Pathogenic Escherichia coli.
      Title: RfaH Counter-Silences Inhibition of Transcript Elongation by H-NS-StpA Nucleoprotein Filaments in Pathogenic Escherichia coli.
    2. Structural and thermodynamic analyses of the beta-to-alpha transformation in RfaH reveal principles of fold-switching proteins.
      Title: Structural and thermodynamic analyses of the β-to-α transformation in RfaH reveal principles of fold-switching proteins.
    3. Allosteric couplings upon binding of RfaH to transcription elongation complexes.
      Title: Allosteric couplings upon binding of RfaH to transcription elongation complexes.
    4. Origins and Molecular Evolution of the NusG Paralog RfaH.
      Title: Origins and Molecular Evolution of the NusG Paralog RfaH.
    5. Structural fluctuations and mechanical stabilities of the metamorphic protein RfaH.
      Title: Structural fluctuations and mechanical stabilities of the metamorphic protein RfaH.
    6. Strikingly, the non-template DNA forms a hairpin in the RfaH:ops complex structure, flipping out a conserved T residue that is specifically recognized by RfaH. Molecular modeling and genetic evidence support the notion that ops hairpin is required for RfaH recruitment.
      Title: The universally-conserved transcription factor RfaH is recruited to a hairpin structure of the non-template DNA strand.
    7. In contrast to NusG, which freely binds to RNA polymerase, RfaH exists in a structurally distinct autoinhibitory state in which the RNA polymerase-binding site is buried at the interface between two RfaH domains.
      Title: Flipping states: a few key residues decide the winning conformation of the only universally conserved transcription factor.
    8. The presence of the leucine-rich element in the RfaH C-terminal domain may be responsible for its flexible structural behavior.
      Title: Structural conversion of the transformer protein RfaH: new insights derived from protein structure prediction and molecular dynamics simulations.
    9. Data indicate that the RfaH transcriptional regulator protein beta-barrel conformation is much more stable than the alpha-helix conformation.
      Title: Molecular dynamics study on folding and allostery in RfaH.
    10. The importance of interfacial interactions between the two domains of RfaH is highlighted by the compromised structural integrity of the helical form of the C-terminal doamin in the absence N-terminal domain.
      Title: Molecular dynamics investigations of the α-helix to β-barrel conformational transformation in the RfaH transcription factor.
    Submit: New GeneRIF Correction See all GeneRIFs (19)

    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 bacterial-type RNA polymerase core enzyme binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables regulatory RNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables transcription antitermination factor activity, DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables transcription antitermination factor activity, DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables translation activator activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA-templated transcription elongation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in DNA-templated transcription elongation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of translation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in transcription antitermination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in transcription antitermination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in transcription antitermination IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in transcription elongation-coupled chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    transcription antiterminator RfaH

    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
      4024333..4024821 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NP_418284.1 transcription antiterminator RfaH [Escherichia coli str. K-12 substr. MG1655]

      See identical proteins and their annotated locations for NP_418284.1

      Status: PROVISIONAL

      UniProtKB/TrEMBL
      A0A376L459
      Conserved Domains (1) summary
      PRK09014
      Location:1 → 162
      rfaH; transcription/translation regulatory transformer protein RfaH
    Nucleotide Protein
    Heading Accession and Version

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