Comparison of the Local Concentration of the HU Protein for Particular Regions of Genomic DNA in Escherichia coli Cells in Vivo

Abstract

HU, a nonspecific histone-like DNA-binding protein, is a major component of the bacterial nucleoid. HU is referred to as an accessory factor in forming and maintaining specific DNA conformations in complex DNA-protein assemblies and as a protein involved in DNA compaction. The HU distribution along the bacterial chromosome in vivo was studied by comparing the local concentration of HU for individual DNA sequences. The method included covalent fixation of DNA-protein contacts with formaldehyde and immuno-precipitation of covalent DNA-protein complexes with anti-HU antibodies. The HU local concentration was assayed in Escherichia coli cells during exponential or stationary growth and was compared for the origin of replication oriC; the promoter and structural regions of hupA and hupB, which code for HU subunits; and the structural regions of dps and glgS, which are activated at the stationary growth phase. During exponential growth, the local concentration of HU was much the same on all DNA sequences examined and did not depend on the transcriptional activity of the genes. During the stationary phase, the HU local concentration was similarly equal on all sequences but was two times higher than at the exponential phase.