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Indirect recognition in sequence-specific DNA binding by Escherichia coli integration host factor: the role of DNA deformation energy.

Kimberly A Aeling·Michael L Opel·Nicholas R Steffen·Vira Tretyachenko-Ladokhina·G Wesley Hatfield·Richard H Lathrop·Donald F Senear
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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.

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Amino Acid MotifsBase SequenceBinding SitesCrystallography, X-RayDNADNA, SuperhelicalEscherichia coliHistonesIntegration Host FactorsModels, MolecularModels, StatisticalMolecular Sequence DataNucleic Acid ConformationRegression AnalysisThermodynamicsJournal ArticleResearch Support, N.I.H., ExtramuralResearch Support, U.S. Gov't, Non-P.H.S.

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Kimberly A Aeling, Michael L Opel, Nicholas R Steffen, Vira Tretyachenko-Ladokhina, G Wesley Hatfield, Richard H Lathrop, Donald F Senear. 2006-10-11. Indirect recognition in sequence-specific DNA binding by Escherichia coli integration host factor: the role of DNA deformation energy.. https://doi.org/10.1074/jbc.m606363200

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