Biology subjects

Romashin, D. D.

Publications and source records attributed to Romashin, D. D..

2 recordsLinked to original sources

bioRxiv2024

Macrolactin A Is an Inhibitor of Protein Biosynthesis in Bacteria

The macrolide antibiotic, macrolactin A (McA), has been known for its antimicrobial properties since the late 1980s, but the mechanism of its antibacterial activity is still unknown. In this study, we investigated the microbiological and molecular characteristics of McA antimicrobial activity. McA effect on bacteria was found to be both bacteriostatic and bactericidal, depending on species and strains. Regarding the mechanism of action of McA, the following important results were obtained: 1) using in vivo and in vitro systems, we showed that McA is an inhibitor of protein synthesis in bacteria; 2) the concentration of McA required to inhibit protein synthesis in the E. coli cell-free model was found to be 50 times lower than the concentration required in the S. aureus cell-free model; 3) the toe-printing assay revealed that McA inhibits the first step of elongation stage of protein synthesis; 4) we identified single and multiple nucleotide polymorphisms in the gene encoding the translation elongation factor Tu (EF-Tu) by annotating the genomes of McA-resistant Bacillus pumilus McAR and its parental strain. Molecular modeling showed that the McA molecule can form non-covalent bonds with amino acids at the interface of domains 1 and 2 of EF-Tu, characterized by a relatively high docking score. Overall, our study demonstrated that McA acts as an elfamycin-like antibiotic (targeting EF-Tu), addressing a substantial gap in our understanding of the mechanism of action of macrolactin A, a representative member of macrolides.

microbiology↗

bioRxiv2020

Role of Udd protein and heterochromatin in transcriptional selection of individual rRNA genes in the Drosophila germline

Eukaryotic genomes contain hundreds of nearly identical rRNA genes, many of which are transcriptionally silent. However, the mechanisms of selective regulation of individual rDNA units remain poorly understood. In Drosophila melanogaster, rDNA repeats containing insertions of R1/R2 retrotransposons within the 28S rRNA sequence undergo inactivation. Here we found that rRNA genes with insertions are specifically enriched with H3K9me3 and HP1a repressive marks, but disruption of heterochromatin components only slightly affects their silencing. Intriguingly, the loss of Udd (Under-developed) protein interacting with Pol I transcription initiation complex, causes an upregulation of R2-inserted rDNA copies in germ cells by two orders of magnitude that is accompanied by the reduction of heterochromatin marks. Thus, for the first time we revealed a factor required for distinguishing between active and silent rDNA units to such a large extent. To clarify a relationship between the rDNA transcriptional status and heterochromatin establishment, we showed that inhibition of transcription by actinomycin D increases the level of H3K9me3 mark erasing the epigenetic differences between inserted and uninserted rRNA genes. Altogether, we suggest that Udd coupled with Pol I transcription initiation machinery defines activation or silencing of individual rDNA units, whereas their transcription level consequently dictates their chromatin state.

molecular biology↗