Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12

Nucleic Acids Res. 2012 Apr;40(8):3524-37. doi: 10.1093/nar/gkr1236. Epub 2011 Dec 17.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosomes, Bacterial / metabolism
  • DNA, Bacterial / metabolism
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism*
  • DNA-Binding Proteins / physiology
  • Escherichia coli K12 / genetics*
  • Escherichia coli K12 / metabolism
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism*
  • Escherichia coli Proteins / physiology
  • Gene Deletion
  • Gene Expression Regulation, Bacterial*
  • Genome, Bacterial
  • Integration Host Factors / genetics
  • Integration Host Factors / metabolism*
  • Integration Host Factors / physiology
  • Protein Multimerization
  • Protein Subunits / genetics
  • Protein Subunits / metabolism
  • Protein Subunits / physiology
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*
  • Transcription Factors / physiology

Substances

  • DNA, Bacterial
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • HupB protein, E coli
  • Integration Host Factors
  • Protein Subunits
  • Transcription Factors
  • hns protein, E coli
  • integration host factor, E coli