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hupA DNA-binding protein HU-alpha [ Escherichia coli str. K-12 substr. MG1655 ]

Gene ID: 948499, updated on 26-Mar-2025

Summary

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Official Symbol
hupA
Official Full Name
DNA-binding protein HU-alpha
Primary source
ECOCYC:EG10466
Locus tag
b4000
See related
ASAP:ABE-0013077
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
ECK3992
Summary
HU concentration in the cell determines the mechanical effect; flexible bends responsible for compaction occur at concentrations <100nM, while increased concentrations result in the formation of a rigid nucleoprotein filament and no significant concentration. [More information is available at EcoGene: EG10466]. HU is a heterodimer formed by an - and a -subunit that are encoded by hupA and hupB genes, respectively. [More information is available at EcoCyc: EG10466].
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Genomic context

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Sequence:
NC_000913.3 (4200281..4200553)

NC_000913.3Genomic Context describing neighboring genes Neighboring gene endonuclease V Neighboring gene DUF416 domain-containing protein YjaG Neighboring gene DUF1481 domain-containing protein YjaH Neighboring gene signaling pathway modulator ZraP

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. HU content and dynamics in Escherichia coli during the cell cycle and at different growth rates. Abebe AH, et al. FEMS Microbiol Lett, 2017 Oct 16. PMID 28961819, Free PMC Article
  2. Conversion of commensal Escherichia coli K-12 to an invasive form via expression of a mutant histone-like protein. Koli P, et al. mBio, 2011. PMID 21896677, Free PMC Article
  3. Right-handed DNA supercoiling by an octameric form of histone-like protein HU: modulation of cellular transcription. Kar S, et al. J Biol Chem, 2006 Dec 29. PMID 17062578
  4. HU-GFP and DAPI co-localize on the Escherichia coli nucleoid. Wery M, et al. Biochimie, 2001 Feb. PMID 11278069
  5. Cocaine babies in Oklahoma. Giacoia GP. J Okla State Med Assoc, 1990 Feb. PMID 2308022

See all (98) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. HU-AB simulacrum: Fusion of HU-B and HU-A into HU-B-A, a functional analog of the Escherichia coli HU-AB heterodimer.
    Title: HU-AB simulacrum: Fusion of HU-B and HU-A into HU-B-A, a functional analog of the Escherichia coli HU-AB heterodimer.
  2. The cellular HUalpha content is proportional to the cell size, whereas its concentration is size independent.
    Title: HU content and dynamics in Escherichia coli during the cell cycle and at different growth rates.
  3. By performing ChIP-seq experiments of each subunit of HU in the absence of the other subunit, genome-wide maps of DNA binding of the proteins in their hetero- and homodimeric forms were defined.
    Title: Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12.
  4. Using the E. coli K-12/HUalpha(E38K, V42L) variant as a model, the authors propose that traditional commensal E. coli can adopt an invasive lifestyle through reprogramming its cellular transcription, without gross genetic changes.
    Title: Conversion of commensal Escherichia coli K-12 to an invasive form via expression of a mutant histone-like protein.
  5. It is remarkable that the observed salt concentration dependency of the binding constants of the three DNA binding modes of the HUalpha subunit is similar, given the large differences in the binding site sizes between these modes.
    Title: Nonspecific DNA binding and bending by HUαβ: interfaces of the three binding modes characterized by salt-dependent thermodynamics.
  6. Under physiological conditions, the three possible dimeric forms of the E. coli HU protein (EcHUalpha, EcHUbeta, and EcHUalphabeta) are in thermal equilibrium between two dimeric conformations (N<--> I) varying in their secondary structure content.
    Title: An alternative flexible conformation of the E. coli HUβ₂ protein: structural, dynamics, and functional aspects.
  7. HU(alphabeta) interacts with duplex DNA using three different nonspecific binding modes
    Title: DNA binding mode transitions of Escherichia coli HU(alphabeta): evidence for formation of a bent DNA--protein complex on intact, linear duplex DNA.
  8. observations support a model whereby DnaA interacts with the HU alpha dimer or the alphabeta heterodimer, depending on their cellular abundance, to recruit the respective form of HU to oriC
    Title: Escherichia coli DnaA interacts with HU in initiation at the E. coli replication origin.
  9. An HU dimer requires 24 nt of ssDNA for initial binding, and 12 nt of ssDNA for each additional dimer binding.
    Title: HU binds and folds single-stranded DNA.
  10. N-terminus verified by Edman degradation on complete protein
    Title: Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12.
Submit: New GeneRIF Correction See all GeneRIFs (11)

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 IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables structural constituent of chromatin IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within DNA damage response IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in DNA repair NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in DNA replication initiation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in DNA replication initiation NAS
Non-traceable Author Statement
more info
 PubMed 
acts_upstream_of_or_within DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within DNA-templated transcription IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in bacterial nucleoid DNA packaging NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in chromosome condensation IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of DnaA-HU complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of HU-DNA complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of HU-DNA complex IPI
Inferred from Physical Interaction
more info
 PubMed 
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 membrane HDA PubMed 
located_in nucleoid IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
DNA-binding protein HU-alpha

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
    4200281..4200553
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NP_418428.1 DNA-binding protein HU-alpha [Escherichia coli str. K-12 substr. MG1655]

    See identical proteins and their annotated locations for NP_418428.1

    Status: PROVISIONAL

    UniProtKB/TrEMBL
    A0A8S0FEI3
    Conserved Domains (1) summary
    PRK10753
    Location:1 → 90
    PRK10753; DNA-binding protein HU-alpha
Nucleotide Protein
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