Dps is a multifunctional homododecameric protein that oxidizes Fe²⁺ ions accumulating them in the form of Fe₂O₃ within its protein cavity, interacts with DNA tightly condensing bacterial nucleoid upon starvation and performs some other functions. During the last two decades from discovery of this protein, its ferroxidase activity became rather well studied, but the mechanism of Dps interaction with DNA still remains enigmatic. The crucial role of lysine residues in the unstructured N-terminal tails led to the conventional point of view that Dps binds DNA without sequence or structural specificity. However, deletion of dps changed the profile of proteins in starved cells, SELEX screen revealed genomic regions preferentially bound in vitro and certain affinity of Dps for artificial branched molecules was detected by atomic force microscopy. Here we report a non-random distribution of Dps binding sites across the bacterial chromosome in exponentially growing cells and show their enrichment with inverted repeats prone to form secondary structures. We found that the Dps-bound regions overlap with sites occupied by other nucleoid proteins, and contain overrepresented motifs typical for their consensus sequences. Of the two types of genomic domains with extensive protein occupancy, which can be highly expressed or transcriptionally silent only those that are enriched with RNA polymerase molecules were preferentially occupied by Dps. In the dps-null mutant we, therefore, observed a differentially altered expression of several targeted genes and found suppressed transcription from the dps promoter. In most cases this can be explained by the relieved interference with Dps for nucleoid proteins exploiting sequence-specific modes of DNA binding. Thus, protecting bacterial cells from different stresses during exponential growth, Dps can modulate transcriptional integrity of the bacterial chromosome hampering RNA biosynthesis from some genes via competition with RNA polymerase or, vice versa, competing with inhibitors to activate transcription.

Multifunctional protein Dps plays an important role in iron assimilation and a crucial role in bacterial genome packaging. Its monomers form dodecameric spherical particles accumulating ~400 molecules of oxidized iron ions within the protein cavity and applying a flexible N-terminal ends of each subunit for interaction with DNA. Deposition of iron is a well-studied process by which cells remove toxic Fe²⁺ ions from the genetic material and store them in an easily accessible form. However, the mode of interaction with linear DNA remained mysterious and binary complexes with Dps have not been characterized so far. It is widely believed that Dps binds DNA without any sequence or structural preferences but several lines of evidence have demonstrated its ability to differentiate gene expression, which assumes certain specificity. Here we show that Dps has a different affinity for the two DNA fragments taken from the dps gene regulatory region. We found by atomic force microscopy that Dps predominantly occupies thermodynamically unstable ends of linear double-stranded DNA fragments and has high affinity to the central part of the branched DNA molecule self-assembled from three single-stranded oligonucleotides. It was proposed that Dps prefers binding to those regions in DNA that provide more contact pads for the triad of its DNA-binding bundle associated with one vertex of the protein globule. To our knowledge, this is the first study revealed the nucleoid protein with an affinity to branched DNA typical for genomic regions with direct and inverted repeats. As a ubiquitous feature of bacterial and eukaryotic genomes, such structural elements should be of particular care, but the protein system evolutionarily adapted for this function is not yet known, and we suggest Dps as a putative component of this system.

In the present article, the possible mitigation of the toxic effect of imidacloprid low-concentration chronic exposure on Danio rerio by the probiotic strain Lactobacillus brevis 47f (1 × 10⁸ CFU/g) was examined. It was found that even sublethal concentration (2500 µg/L) could lead to the death of some fish during the 60-day chronic experiment. However, the use of Lactobacillus brevis 47f partially reduced the toxic effects, resulting in an increased survival rate and a significant reduction of morphohistological lesions in the intestines and kidneys of Danio rerio. The kidneys were found to be the most susceptible organ to toxic exposure, showing significant disturbances. Calculation of the histopathological index, measurement of morphometric parameters, and analysis of principal components revealed the most significant parameters affected by the combined action of imidacloprid and Lactobacillus brevis 47f. This effect of imidacloprid and the probiotic strain had a multidirectional influence on various pro/anti-inflammatory cytokines (IL-1β, TNF-α, IL-6, IL-8). Therefore, the results suggest the possibility of further studying the probiotic strain Lactobacillus brevis 47f as a strain that reduces the toxic effects of xenobiotics. Additionally, the study established the possibility of using imidacloprid as a model toxicant to assess the detoxification ability of probiotics on the kidney and gastrointestinal tract of fish.

The novelty of the work lies in the creation and study of the physical and biological properties of biodegradable polymer coatings for stents based on poly(lactic-co-glycolic acid) (PLGA). Polymer coatings are capable of prolonged and directed release of molecules with a high molecular weight, in particular, protein molecules of prourokinase (m.w. 54 kDa). A technology has been developed to create coatings having a relative elongation of 40% to 165% and a tensile strength of 25–65 MPa. Coatings are biodegradable; the rate of degradation of the polymer in an isotonic solution varies in the range of 0.05%–1.0% per day. The created coatings are capable of controlled release of the protein of prourokinase, while about 90% of the molecules of prourokinase retain their enzymatic activity. The rate of release of prourokinase can vary from 0.01 to 0.08 mg/day/cm². Coatings do not have a short-term toxic effect on mammalian cells. The mitotic index of cells growing on coatings is approximately 1.5%. When implanting the developed polymers in animals in the postoperative period, there are no complications. Histological examination did not reveal pathological processes. When implanting individual polymers 60 days after surgery, only traces of PLGA are detected. Thus, a biodegradable composite mechanically resistant polymer capable of prolonged release of the high molecular weight prourokinase enzyme has been developed.