Indirect recognition in sequence-specific DNA binding by Escherichia coli integration host factor: the role of DNA deformation energy.
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.
Aeling
Kimberly A
KA
Institute for Genomics and Bioinformatics, Department of Microbiology and Molecular Genetics, School of Medicine, University of California 92697, USA.
Opel
Michael L
ML
Steffen
Nicholas R
NR
Tretyachenko-Ladokhina
Vira
V
Hatfield
G Wesley
GW
Lathrop
Richard H
RH
Senear
Donald F
DF
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
D004278:DNA, Superhelical; D006657:Histones; D034982:Integration Host Factors; D004247:DNA