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stpA DNA-binding transcriptional repressor StpA with RNA chaperone activity [ Escherichia coli str. K-12 substr. MG1655 ]

Gene ID: 947130, updated on 3-Dec-2024

Summary

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Official Symbol
stpA
Official Full Name
DNA-binding transcriptional repressor StpA with RNA chaperone activity
Primary source
ECOCYC:EG11554
Locus tag
b2669
See related
ASAP:ABE-0008788
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
ECK2663; hnsB
Summary
StpA binds prefereably unstructured RNA weakly, with mainly electrostatic interactions that promote RNA folding (Mayer, 2007). [More information is available at EcoGene: EG11554]. StpA is a DNA-binding protein with similarity to H-NS. [More information is available at EcoCyc: EG11554].
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Genomic context

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Sequence:
NC_000913.3 (2798091..2798495, complement)

NC_000913.3Genomic Context describing neighboring genes Neighboring gene putative DNA-binding transcriptional regulator YgaV Neighboring gene thiosulfate sulfurtransferase YgaP Neighboring gene L-alanine exporter Neighboring gene DUF2002 domain-containing protein YgaC

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. The RNA chaperone StpA enables fast RNA refolding by destabilization of mutually exclusive base pairs within competing secondary structure elements. Hohmann KF, et al. Nucleic Acids Res, 2021 Nov 8. PMID 34614185, Free PMC Article
  2. StpA protein from Escherichia coli condenses supercoiled DNA in preference to linear DNA and protects it from digestion by DNase I and EcoKI. Keatch SA, et al. Nucleic Acids Res, 2005. PMID 16299353, Free PMC Article
  3. Influence of RNA structural stability on the RNA chaperone activity of the Escherichia coli protein StpA. Grossberger R, et al. Nucleic Acids Res, 2005. PMID 15849314, Free PMC Article
  4. Folding of the td pre-RNA with the help of the RNA chaperone StpA. Mayer O, et al. Biochem Soc Trans, 2002 Nov. PMID 12440999
  5. RNA chaperone StpA loosens interactions of the tertiary structure in the td group I intron in vivo. Waldsich C, et al. Genes Dev, 2002 Sep 1. PMID 12208852, Free PMC Article

See all (62) 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. The RNA chaperone StpA enables fast RNA refolding by destabilization of mutually exclusive base pairs within competing secondary structure elements.
    Title: The RNA chaperone StpA enables fast RNA refolding by destabilization of mutually exclusive base pairs within competing secondary structure elements.
  3. StpA represses CRISPR-Cas immunity in H-NS deficient Escherichia coli.
    Title: StpA represses CRISPR-Cas immunity in H-NS deficient Escherichia coli.
  4. Hha and StpA greatly enhance H-NS-stimulated pausing by RNAP at 20 degrees C. StpA:H-NS or StpA-only filaments also stimulate pausing at 37 degrees C, a temperature at which Hha:H-NS or H-NS-only filaments have much less effect. In addition, both Hha and StpA greatly stimulate DNA-DNA bridging by H-NS filaments.
    Title: StpA and Hha stimulate pausing by RNA polymerase by promoting DNA-DNA bridging of H-NS filaments.
  5. three new candidates of E. coli nucleoid, namely DNA-binding protein from starved cells (Dps), host factor for phage Qbeta (Hfq) and suppressor of td(-) phenotype A (StpA)
    Title: Growth phase dependent changes in the structure and protein composition of nucleoid in Escherichia coli.
  6. Also, DeltahnsDeltastpA double mutants simultaneously lacking H-NS and its paralog StpA showed more severe reductions in ompW expression at 37 degrees C, resulting in the complete loss of OmpW.
    Title: Expression of the Escherichia coli ompW colicin S4 receptor gene is regulated by temperature and modulated by the H-NS and StpA nucleoid-associated proteins.
  7. Both the DNA binding sites of H-NS as well as the function of StpA as a backup system might be selected for silencing highly transcribable genes.
    Title: Genomic analysis reveals epistatic silencing of "expensive" genes in Escherichia coli K-12.
  8. In contrast to H-NS, the StpA filament interacts with a naked DNA segment to cause DNA bridging which results in simultaneous stiffening and bridging of DNA.
    Title: Gene silencing H-NS paralogue StpA forms a rigid protein filament along DNA that blocks DNA accessibility.
  9. StpA binding profile reduced to one-third in the hns mutant and the H-NS binding profile was unaffected by stpA inactivation.
    Title: Differential binding profiles of StpA in wild-type and h-ns mutant cells: a comparative analysis of cooperative partners by chromatin immunoprecipitation-microarray analysis.
  10. StpA in homologous recombination and double-strand break repair is discussed
    Title: Roles of the DNA binding proteins H-NS and StpA in homologous recombination and repair of bleomycin-induced damage in Escherichia coli.
Submit: New GeneRIF Correction See all GeneRIFs (17)

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 IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription repressor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables bent DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables minor groove of adenine-thymine-rich DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein dimerization activity IEA
Inferred from Electronic Annotation
more info
  
enables structural constituent of chromatin IEA
Inferred from Electronic Annotation
more info
  
enables transcription cis-regulatory region binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in negative regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoid IEA
Inferred from Electronic Annotation
more info
  
part_of protein-DNA complex IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
DNA-binding transcriptional repressor StpA with RNA chaperone activity

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
    2798091..2798495 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NP_417155.1 DNA-binding transcriptional repressor StpA with RNA chaperone activity [Escherichia coli str. K-12 substr. MG1655]

    See identical proteins and their annotated locations for NP_417155.1

    Status: PROVISIONAL

    UniProtKB/TrEMBL
    A0A5B9APP6
    Conserved Domains (1) summary
    PRK10328
    Location:1 → 134
    PRK10328; DNA-binding protein StpA
Nucleotide Protein
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