title: Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12.
abstract: IHF and HU are two heterodimeric nucleoid-associated proteins (NAP) that belong to the same protein family but interact differently with the DNA. IHF is a sequence-specific DNA-binding protein that bends the DNA by over 160°. HU is the most conserved NAP, which binds non-specifically to duplex DNA with a particular preference for targeting nicked and bent DNA. Despite their importance, the in vivo interactions of the two proteins to the DNA remain to be described at a high resolution and on a genome-wide scale. Further, the effects of these proteins on gene expression on a global scale remain contentious. Finally, the contrast between the functions of the homo- and heterodimeric forms of proteins deserves the attention of further study. Here we present a genome-scale study of HU- and IHF binding to the Escherichia coli K12 chromosome using ChIP-seq. We also perform microarray analysis of gene expression in single- and double-deletion mutants of each protein to identify their regulons. The sequence-specific binding profile of IHF encompasses ∼30% of all operons, though the expression of <10% of these is affected by its deletion suggesting combinatorial control or a molecular backup. The binding profile for HU is reflective of relatively non-specific binding to the chromosome, however, with a preference for A/T-rich DNA. The HU regulon comprises highly conserved genes including those that are essential and possibly supercoiling sensitive. Finally, by performing ChIP-seq experiments, where possible, of each subunit of IHF and HU in the absence of the other subunit, we define genome-wide maps of DNA binding of the proteins in their hetero- and homodimeric forms.
authors.affiliation: Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK.
authors.forename: Ana I
authors.initials: AI
authors.lastname: Prieto
authors.forename: Christina
authors.initials: C
authors.lastname: Kahramanoglou
authors.forename: Ruhi M
authors.initials: RM
authors.lastname: Ali
authors.forename: Gillian M
authors.initials: GM
authors.lastname: Fraser
authors.forename: Aswin S N
authors.initials: AS
authors.lastname: Seshasayee
authors.forename: Nicholas M
authors.initials: NM
authors.lastname: Luscombe
mesh_terms: D002876:Chromosomes, Bacterial / Q000378:metabolism; D004269:DNA, Bacterial / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism* / Q000502:physiology; D048168:Escherichia coli K12 / Q000235:genetics* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism* / Q000502:physiology; D017353:Gene Deletion; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D034982:Integration Host Factors / Q000235:genetics / Q000378:metabolism* / Q000502:physiology; D055503:Protein Multimerization; D021122:Protein Subunits / Q000235:genetics / Q000378:metabolism / Q000502:physiology; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism* / Q000502:physiology
chemical_list: D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; C541388:HupB protein, E coli; D034982:Integration Host Factors; D021122:Protein Subunits; D014157:Transcription Factors; C116822:hns protein, E coli; C440502:integration host factor, E coli