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

    Gene ID: 948499, updated on 3-Dec-2024

    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. HU-GFP and DAPI co-localize on the Escherichia coli nucleoid. Wery M, et al. Biochimie, 2001 Feb. PMID 11278069
    4. 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
    5. Cocaine babies in Oklahoma. Giacoia GP. J Okla State Med Assoc, 1990 Feb. PMID 2308022

    See all (97) 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 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
    Heading Accession and Version

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