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Histone-like HU proteins are global regulators of the topology of the bacterial genome and are involved in transcriptional regulation. These proteins are essential for the survival of the simplest free-living microorganisms of the Mollicutes class and a number of pathogenic bacteria, including Mycobacterium tuberculosis and Streptococcus pneumonia, and are promising targets for the design of new antibiotics. However, the competitive inhibition of the DNA-binding ability of HU proteins is inefficient because of high flexibility and the large size of the DNA-binding site. Hence, an alternative approach was employed based on searching for molecules targeting the interface between two monomers. The three-dimensional structure of the HU protein from Spiroplasma melliferum (HUSpm) was used as a target for the virtual screening of the compound library and for the modeling of HUSpm in complex with the inhibitor. An analysis of the molecular dynamics trajectory calculated for the HUSpm–inhibitor complex confirmed the fact that the binding of the inhibitor at the interface between monomers leads to the disruption of conformational dynamics in the region of the DNA-binding domain. The gel retardation assay showed that the inhibitor actually disturbs DNA-binding activity of the protein, thereby indicating that this is a promising approach.

Histone-like protein HU is a dimeric nucleoid-associated protein (NAP). HU is the most conserved NAP. It binds nonspecifically to duplex DNA with a preference for targeting nicked and bent DNA. HU limits the architecture of the bacterial nucleoid and its deletion is lethal for Bacillus subtilis and Mycoplasma genitalium which do not contain other NAPs. E. coli lacking HU is viable but has numerous growth defects. The effects of the HU protein on gene expression is known from microarray analysis and HU regulons were identified. In HU-deficient E. coli, absence of this DNA architectural protein causes a disorder in gene regulation; on the other hand, E. coli growth under standard conditions is almost unaltered in the absence of HU. To understand how the bacterium confronts the chromosomal disorder, we performed proteome analysis to compare protein abundances in cells containing the HU protein or not. Comparison of the proteomic profile of wild-type and HU-deficient E. coli shows how the altered gene expression influences the protein content. We show that proteome profile changes are very similar to the gene expression profile changes in HU-deficient E. coli. Several exceptions show that proteome studies are very important.