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PMID: 8262044 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Specific interaction of IHF with RIBs, a class of bacterial repetitive DNA elements located at the 3' end of transcription units.

The EMBO journal ·Vol. 12 ·No. 13 ·1993-12-15 ·Pages 5019-27

Boccard F, Prentki P

Abstract

The prokaryotic REP (repetitive extragenic palindromes) or PU (palindromic units) sequences are often associated with other repetitive elements, forming arrangements which have been called 'BIMEs' (bacterial interspersed mosaic elements). It is estimated that the Escherichia coli chromosome carries approximately 300-500 BIMEs, whose biological role is at present unknown. We have identified a family of BIMEs consisting of two converging REP sequences flanking a 35 bp conserved segment which carries a static DNA bend and a binding site for IHF, the integration host factor of E.coli. We estimate that the E.coli genome harbors approximately 100 copies of this module, which we name 'RIB' (reiterative ihf BIME). We have analyzed by gel retardation and by footprinting the in vitro interaction of IHF with individual RIBs, and shown that the protein binds strongly and specifically to their center. We have also demonstrated binding of IHF to the chromosomal population of RIBs, using a new approach which combines two-dimensional bandshift and Southern blotting. RIB elements are at the end of transcription units, and thus define a new class of ihf sites. Possible implications for genome structure and DNA topology are discussed.

MeSH Terms
Bacterial Proteins/metabolism Base Sequence Binding Sites Consensus Sequence DNA Primers/chemistry DNA, Bacterial/metabolism DNA-Binding Proteins/metabolism Escherichia coli/genetics Gene Expression Regulation, Bacterial Genes, Bacterial Integration Host Factors Membrane Proteins/genetics Molecular Sequence Data Protein Binding Repetitive Sequences, Nucleic Acid Transcription, Genetic
Chemicals
Bacterial Proteins DNA Primers DNA, Bacterial DNA-Binding Proteins Integration Host Factors Membrane Proteins
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Boccard F
Department of Molecular Biology, University of Geneva, Switzerland.
Prentki P
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Article Info
Journal
The EMBO journal
Abbr.
EMBO J
ISSN
0261-4189
Published
1993-12-15
Pages
5019-27
Language
English
Region
England
NLM ID
8208664
PMCID
PMC413762
Subset
IM
External Links
PubMed source PMC Full Text View journal details
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