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J Biol Chem, Vol. 274, Issue 46, 33105-33113, November 12, 1999
From the The genome of Escherichia coli is
composed of a single molecule of circular DNA with the length of about
47,000 kilobase pairs, which is associated with about 10 major
DNA-binding proteins, altogether forming the nucleoid. We expressed and
purified 12 species of the DNA-binding protein, i.e. CbpA
(curved DNA-binding protein A), CbpB or Rob (curved DNA-binding protein
B or right arm of the replication origin binding protein), DnaA
(DNA-binding protein A), Dps (DNA-binding protein from starved cells),
Fis (factor for inversion stimulation), Hfq (host factor for phage Q
Twelve Species of the Nucleoid-associated Protein from
Escherichia coli
SEQUENCE RECOGNITION SPECIFICITY AND DNA BINDING AFFINITY
§ and
Department of Molecular Genetics, National
Institute of Genetics, Mishima, Shizuoka 411-8540, Japan and the
§ Japan Science and Technology Corporation, Kawaguchi,
Saitama 332-0012, Japan
), H-NS (histone-like nucleoid structuring protein), HU (heat-unstable nucleoid protein), IciA (inhibitor of chromosome initiation A), IHF (integration host factor), Lrp (leucine-responsive regulatory protein), and StpA (suppressor of
td
phenotype A). The sequence specificity of
DNA binding was determined for all the purified nucleoid proteins using
gel-mobility shift assays. Five proteins (CbpB, DnaA, Fis, IHF, and
Lrp) were found to bind to specific DNA sequences, while the remaining
seven proteins (CbpA, Dps, Hfq, H-NS, HU, IciA, and StpA) showed
apparently sequence-nonspecific DNA binding activities. Four proteins,
CbpA, Hfq, H-NS, and IciA, showed the binding preference for the curved
DNA. From the apparent dissociation constant (Kd)
determined using the sequence-specific or nonspecific DNA probes, the
order of DNA binding affinity were determined to be: HU > IHF > Lrp > CbpB(Rob) > Fis > H-NS > StpA > CbpA > IciA > Hfq/Dps, ranging
from 25 nM (HU binding to the non-curved DNA) to 250 nM (Hfq binding to the non-curved DNA), under the assay
conditions employed.
Copyright © 1999 by The American Society for Biochemistry and Molecular Biology, Inc.
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