Biology subjects

Alekseev, A. A.

Publications and source records attributed to Alekseev, A. 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

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

Properties of the Ureaplasma parvum SMC protein related to its interaction with DNA

SMC (Structural Maintenance of Chromosomes) ATPase proteins are integral components of complexes bearing the same name, crucial for the spatial organization of DNA across diverse life forms, spanning bacteria, archaea, and eukaryotes. It is proposed that in bacteria, SMC complexes facilitate DNA compaction through loop extrusion and aid in the segregation of daughter nucleoids. In this paper the properties of the SMC ATPase protein from Ureaplasma parvum were investigated by using a spectrum of methods, including conventional biochemical methods as well as advanced single-molecule techniques. Our findings reveal distinctive properties of this protein compared to its extensively studied homologue from Bacillus subtilis. Notably, our results suggest that U. parvum SMC ATPase facilitates DNA compaction even in the absence of ATP.

molecular biology↗

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↗

bioRxiv2023

Optogenetic control of lysosome function

Lysosome protective, metabolic, signaling functions are highly dependent on their pH. A lack of tools of high spatial and temporal resolution for pH control is a bottleneck of lysosome related cell research. Light-driven inward proton pump NsXeR, targeted to the lysosomes of mammalian cells, produces lysosome alkalization simply by light. Complementary use of outward proton pumping Arch3 rhodopsins in lysosomes offers an approach to vary pH in a range from around 5 to 6.5 in both directions (de-acidification and acidification). Lyso-NsXeR optogenetics efficiency was demonstrated, in particular, by its ability to inhibit lysosome proteolytic enzymes. Thus, optogenetic monitoring and regulation of the lysosome function, through pH control over a wide range, could serve as an approach to studying fundamental cell processes, and rational drug design.

cell biology↗