Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12.
Prieto, Ana I
Seshasayee, Aswin SN
Luscombe, Nicholas M
Nucleic acids research
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Prieto, A. I., Kahramanoglou, C., Ali, R., Fraser, G., Seshasayee, A. S., & Luscombe, N. M. (2012). Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12.. Nucleic acids research, 40 (8), 3524-3537. https://doi.org/10.1093/nar/gkr1236
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.
Chromosomes, Bacterial, Escherichia coli K12, Escherichia coli Proteins, Integration Host Factors, DNA-Binding Proteins, Protein Subunits, Transcription Factors, DNA, Bacterial, Gene Expression Regulation, Bacterial, Gene Deletion, Genome, Bacterial, Protein Multimerization
External DOI: https://doi.org/10.1093/nar/gkr1236
This record's URL: https://www.repository.cam.ac.uk/handle/1810/279393
Attribution 4.0 International (CC BY 4.0)
Licence URL: https://creativecommons.org/licenses/by/4.0/