title: Indirect recognition in sequence-specific DNA binding by Escherichia coli integration host factor: the role of DNA deformation energy.
abstract: Integration host factor (IHF) is a bacterial histone-like protein whose primary biological role is to condense the bacterial nucleoid and to constrain DNA supercoils. It does so by binding in a sequence-independent manner throughout the genome. However, unlike other structurally related bacterial histone-like proteins, IHF has evolved a sequence-dependent, high affinity DNA-binding motif. The high affinity binding sites are important for the regulation of a wide range of cellular processes. A remarkable feature of IHF is that it employs an indirect readout mechanism to bind and wrap DNA at both the nonspecific and high affinity (sequence-dependent) DNA sites. In this study we assessed the contributions of pre-formed and protein-induced DNA conformations to the energetics of IHF binding. Binding energies determined experimentally were compared with energies predicted for the IHF-induced deformation of the DNA helix (DNA deformation energy) in the IHF-DNA complex. Combinatorial sets of de novo DNA sequences were designed to systematically evaluate the influence of sequence-dependent structural characteristics of the conserved IHF recognition elements of the consensus DNA sequence. We show that IHF recognizes pre-formed conformational characteristics of the consensus DNA sequence at high affinity sites, whereas at all other sites relative affinity is determined by the deformational energy required for nearest-neighbor base pairs to adopt the DNA structure of the bound DNA-IHF complex.
authors.affiliation: Institute for Genomics and Bioinformatics, Department of Microbiology and Molecular Genetics, School of Medicine, University of California 92697, USA.
authors.forename: Kimberly A
authors.initials: KA
authors.lastname: Aeling
authors.forename: Michael L
authors.initials: ML
authors.lastname: Opel
authors.forename: Nicholas R
authors.initials: NR
authors.lastname: Steffen
authors.forename: Vira
authors.initials: V
authors.lastname: Tretyachenko-Ladokhina
authors.forename: G Wesley
authors.initials: GW
authors.lastname: Hatfield
authors.forename: Richard H
authors.initials: RH
authors.lastname: Lathrop
authors.forename: Donald F
authors.initials: DF
authors.lastname: Senear
mesh_terms: D020816:Amino Acid Motifs; D001483:Base Sequence; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D004278:DNA, Superhelical / Q000737:chemistry; D004926:Escherichia coli / Q000378:metabolism*; D006657:Histones / Q000737:chemistry; D034982:Integration Host Factors / Q000378:metabolism / Q000502:physiology*; D008958:Models, Molecular; D015233:Models, Statistical; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012044:Regression Analysis; D013816:Thermodynamics
chemical_list: D004278:DNA, Superhelical; D006657:Histones; D034982:Integration Host Factors; D004247:DNA