title: In vitro evolution of the DNA binding sites of Escherichia coli methionine repressor, MetJ.
abstract: The SELEX procedure was used to study the recognition between the E. coli methionine repressor (MetJ) and its DNA binding sites. DNA ligands with high affinity for either the holo-repressor or apo-repressor were isolated from a pool of molecules randomized over 20 base-pairs. Among 90 DNA ligands selected by holo-repressor binding, roughly 90% contain variations of two tandem, perfect eight base-pair Met-boxes, which are the consensus deduced from natural met operators. Base-pairs that are important, for specific interactions with the protein are highly conserved. The data also reveal the importance of the non-contacted operator base-pairs in facilitating the conformational changes in the operator which must occur for repressor binding. There are also effects due to the sequences of the base-pairs immediately flanking the operator site. DNA ligands selected by apo-repressor share a very similar, but not identical, consensus with that selected by holo-repressor, suggesting that the corepressor does not greatly alter the specificity of repressor binding.
authors.affiliation: Department of Molecular Cellular and Developmental Biology, University of Colorado at Boulder 80309, USA.
authors.forename: Y Y
authors.initials: YY
authors.lastname: He
authors.forename: P G
authors.initials: PG
authors.lastname: Stockley
authors.forename: L
authors.initials: L
authors.lastname: Gold
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D001482:Base Composition; D001483:Base Sequence; D001665:Binding Sites; D017124:Conserved Sequence; D004269:DNA, Bacterial / Q000378:metabolism*; D019020:Directed Molecular Evolution; D004926:Escherichia coli / Q000235:genetics*; D029968:Escherichia coli Proteins; D008024:Ligands; D008969:Molecular Sequence Data; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism*; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D008024:Ligands; D012097:Repressor Proteins; C060486:methionine repressor protein, Bacteria; C489220:methionine repressor protein, E coli