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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.

Interaction of the Tramtrack protein from Drosophila melanogaster with DNA was analyzed by a cross-linking method. Tramtrack residues cross-linkable to the partially depurinated DNA were identified by direct sequencing. The N-terminal alpha-amino group of the protein DNA-binding domain was found to be the major product of cross-linking. The location of the N terminus on the DNA was determined by identification of the DNA bases that were cross-linked to the protein alpha-amino group. We conclude that accessory N-terminal peptide preceding the first zinc finger of Tramtrack directly interacts with DNA, both in specific and nonspecific DNA-protein complexes. Our finding explains the role in the protein binding of the DNA bases outside of the direct interaction with the zinc fingers.

Along with symmetrical features (palindromes, direct and inverted repeats), periodicities in the disposition of nucleotides in the origin of chromosome replication oriC from E. coli were studied by means of Fourier analysis. Peaks corresponding to the periods T = 2, 17, 95-100 nucleotides are the highest in the Fourier spectrum of oriC. Peaks corresponding to the periods T = 3, 11, 19, 13, 24, 27, 28, 41, 79-81 nucleotides are also prominent, but not so high. Thus, the main periodicities of the oriC spectrum of are not multiple of the B-DNA sugar-phosphate backbone period, which destabilize DNA at oriC and contributes to the spontaneous unwinding of DNA. The differences between the Fourier spectrum of oriC and those of regions adjacent to oriC are demonstrated.

We have identified the lac repressor amino acids which form cross-links with partially depurinated DNA and hence are proximate to it. Only lysine-33 is cross-linkable in specific complex with lac operator. At the presence of inducer molecules lysine-33 remains cross-linkable. However, the N-terminal alpha-aminogroup was additionally cross-linked with the boundaries of lac operator. We conclude that orientation of the DNA-binding domain of the repressor is reversed by inducer binding.