Biology subjects

Khodorkovskii, M. A.

Publications and source records attributed to Khodorkovskii, M. A..

5 recordsLinked to original sources

bioRxiv2026

Poly(ADP-ribose)polymerase1 facilitates the nucleosome disassembly

Being the basic building blocks of chromatin, nucleosomes and their stability determine the genome accessibility for different DNA-dependent proteins. This characteristic is labile under all cell-life processes. One of the abundant DNA-binding proteins, which is important for genome compaction, is poly(ADP-ribose)polymerase1 (PARP1). Despite the extensive experimental data on the chromatin compaction regulation under ADP-ribosylation, the details of the interplay of nucleosome with PARP1 in the absence of protein activation remain unclear. In this study, we analyzed the changes in the nucleosome wrapping upon PARP1 interaction using a single-molecule approach -- optical tweezers. We demonstrate that PARP1 binding leads to weakening of the contacts that support the nucleosome core.

molecular biology↗

bioRxiv2025

Plasmid copy number affects the DNA methylation-driven expression dynamics of the CfrBI restriction-modification system and impacts phage restriction

Restriction-modification (R-M) systems are one of the most widespread and, due to their often plasmid-based nature, transmittable anti-phage systems bacteria have. The CfrBI R-M system studied here consists of a methyltransferase (MT) and a restriction endonuclease (RE) that are divergently expressed and share a promoter region that harbors a single CfrBI recognition site. Previously, the methylation of this site has been shown to regulate the expression of the R-M system. Here, we show that the expression dynamics of the CfrBI R-M system and its protective properties depend on the copy number of the plasmid harboring it. A higher copy number results in higher expression, but the expression on a medium-copy number plasmid interestingly conferred the highest phage resistance. After transformation of naive cells however, expression of the RE was fastest in the high-copy plasmid background. In vivo we show that the expression strength of the MT inhibits its own expression, while enhancing RE expression. To conclude, the results indicate that for phage resistance the overall expression strength might not be the predominant factor in case of the CfrBI R-M system, while for the establishment of the system the initial expression rate of the MT seems to be the determining factor.

microbiology↗

bioRxiv2025

Mycoplasma gallisepticum FtsZ demonstrates properties that distinguish it from other known homologs

In bacteria, cell division usually occurs through binary fission, with the participation of genes from the dcw cluster. In mollicutes, this cluster is significantly reduced -- often only the ftsZ, ftsA, mraZ, and mraW genes remain, and sometimes ftsZ is completely absent. FtsZ is a key division protein that forms the Z-ring, but its role in mollicutes is questionable due to the absence of many cell division proteins and the cell wall. In the current study, we investigated the FtsZ protein of Mycoplasma gallisepticum, a bacterium with a reduced set of putative cell division genes (ftsZ, ftsA, ftsK). The results show that, unlike in well-studied bacteria, FtsZ in M. gallisepticum often exhibits polar rather than mid-cell localization. Overexpression of fluorescently labeled FtsZ enhances this polar localization and may lead to minicell formation. The FtsZ concentration was measured and, together with in vitro data, confirmed its ability to polymerize, similar to its homologs. Protein-protein interactions were also analyzed and confirmed the link of FtsZ to cell division. Overall, the results support the role of FtsZ in cell division, though its properties differ significantly from other known homologs.

molecular biology↗

bioRxiv2025

Interactions of the Escherichia coli SMC-like RecN protein with different forms of DNA revealed at the single-molecule level using optical tweezers

DNA molecule is the storage of genetic information in all living organisms. Its integrity is critical to life. However, due to the exposure to various environmental factors and endogenous agents, double-strand DNA breaks occur. Bacteria are capable to restore their genome integrity through a process called the SOS response. The key protein of SOS response is the RecA recombinase. Also critical for DNA repair is the SMC-like RecN protein, which helps RecA to find the homologous DNA template. Currently, its functions and mechanism of action remain poorly understood. In this work, using optical tweezers, we show predominant binding of RecN to ssDNA and also demonstrate a weak binding of dsDNA causing a condition similar to DNA loops formation.

biophysics↗

bioRxiv2024

Features of the DNA Escherichia coli RecN interaction revealed by fluorescence microscopy and single-molecule methods

The SOS response is a condition that occurs in bacterial cells after DNA damage. In this state, the bacterium is able to recover the integrity of its genome. Due to the increased level of mutagenesis in cells during the repair of DNA double-strand breaks, the SOS response is also an important mechanism for bacterial adaptation to the antibiotics. One of the key proteins of the SOS response is the SMC-like protein RecN, which helps the RecA recombinase to find a homologous DNA template for repair. In this work, the localization of the recombinant RecN protein in living Escherichia coli cells was revealed using fluorescence microscopy. It has been shown that the RecN, outside the SOS response, is predominantly localized at the poles of the cell, and in dividing cells, also localized at the center. Using in vitro methods including fluorescence microscopy and optical tweezers, we show that RecN predominantly binds single-stranded DNA in an ATP-dependent manner. RecN has both intrinsic and single-stranded DNA-stimulated ATPase activity. The results of this work may be useful for better understanding of the SOS response mechanism and homologous recombination process.

molecular biology↗