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

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: REVIEWED
Organism: Escherichia coli str. K-12 substr. MG1655 (strain: K-12, substrain: MG1655)
Lineage: Bacteria; Pseudomonadati; 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_000913.3 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_000913.3

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

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	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	IEA Inferred from Electronic Annotation more info
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
involved_in DNA-templated transcription	IEA Inferred from Electronic Annotation more info
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	IEA Inferred from Electronic Annotation more info
part_of HU-DNA complex	IDA Inferred from Direct Assay more info	PubMed
part_of HU-DNA complex	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 cytosol	IEA Inferred from Electronic Annotation more info
located_in membrane	HDA more info	PubMed
located_in nucleoid	IEA Inferred from Electronic Annotation more info