Major Nucleoid Proteins in the Structure and Function of theEscherichia coliChromosome

Abstract

This chapter focuses on the major nucleoid-associated proteins and summarizes one's current knowledge of how these proteins contribute to the structure of the nucleoid and function in specific reactions involving the chromosome. The current view is that the Escherichia coli nucleoid is dominated by five different proteins: HU, integration host factor (IHF), H-NS, StpA and Fis under nutrient-rich exponential growth conditions. HU mutant cells display the most severe and varied phenotypes in comparison to strains containing mutations in the other major nucleoid proteins. Supercoiling of chromosomal and plasmid DNA is partially relaxed in mutants lacking HU, supporting an in vivo role for HU in regulating the degree of supercoiling. HU plays several interconnected roles in DNA replication and appears to be involved in several steps involving initiation of chromosomal DNA synthesis, chromosomal partitioning, and cell division. The genes that were differentially expressed were examined for putative IHF binding sites in the 500 bp upstream of the transcription initiation site. The criteria for identifying high-affinity sites were that the sites must have a 12 out of 13 bp match with the core consensus sequence and that at least 10 of the 15 bp 5' (upstream) to the core consensus must be dA-dT base pairs. The study identified 46 candidates that matched the criteria, some of which were documented in other studies. The study also identified seven genes, including ihfA, that were expressed only when IHF was present and eight genes that were expressed only in IHF-deficient cells.