Article
Biochemistry & Molecular Biology
Lukasz Mazurek, Dmitry Ghilarov, Elizabeth Michalczyk, Zuzanna Pakosz, Mikhail Metelev, Wojciech Czyszczon, Karolina Wawro, Iraj Behroz, Svetlana Dubiley, Roderich D. Suessmuth, Jonathan G. Heddle
Summary: DNA gyrase, a type II topoisomerase mainly found in bacteria, is targeted by various natural product toxins and synthetic molecules like fluoroquinolones. Pentapeptide repeat proteins (PRPs) can mediate resistance to these toxins, with QnrB1 specifically protecting against fluoroquinolones by stimulating gyrase ATPase activity. The mechanism involves QnrB1 binding to GyrB and promoting fluoroquinolone dissociation from the cleavage complex through allosteric mechanisms.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Cell Biology
Mohamed Rasheed Gadalla, Eliot Morrison, Marina Serebryakova, Xueijiao Han, Thorsten Wolff, Christian Freund, Larisa Kordyukova, Michael Veit
Summary: The study revealed that ZDHHC22 is upregulated in virus-infected cells, particularly with avian influenza virus strains. Knocking out ZDHHC22 gene did not reduce acylation of M2 and HA, indicating its potential involvement in virus replication.
CELLULAR MICROBIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
D. A. Sutormin, A. K. Galivondzhyan, A. V. Polkhovskiy, S. O. Kamalyan, K. V. Severinov, S. A. Dubiley
Summary: The DNA double helix is a simple and elegant way to store and copy genetic information, but processes like transcription and replication can lead to a topological side effect of supercoiling. Topoisomerases are enzymes that help untangle the topological challenges associated with DNA supercoiling by relaxing supercoils and resolving catenanes and knots.
Article
Multidisciplinary Sciences
Anastasiia Grigoreva, Julia Andreeva, Dmitry Bikmetov, Anastasiia Rusanova, Marina Serebryakova, Andrea Hernandez Garcia, Darya Slonova, Satish K. Nair, Guy Lippens, Konstantin Severinov, Svetlana Dubiley
Summary: A new family of class III lanthipeptides from Firmicutes is described, with representative member andalusicin showing bioactivity against various Gram-positive bacteria, which is highly dependent on the alpha-N dimethylation.
Article
Multidisciplinary Sciences
Hana Nuskova, Marina V. Serebryakova, Anna Ferrer-Caelles, Timo Sachsenheimer, Christian Luechtenborg, Aubry K. Miller, Britta Bruegger, Larisa V. Kordyukova, Aurelio A. Teleman
Summary: This study reveals that exposure of cells to different fatty acids affects the acylation of GNAI proteins, altering their function and EGFR pathway activation, thus linking metabolism to signaling pathways.
NATURE COMMUNICATIONS
(2021)
Article
Cell Biology
Jeroen De Smet, Jeroen Wagemans, Maarten Boon, Pieter-Jan Ceyssens, Marleen Voet, Jean-Paul Noben, Julia Andreeva, Dmitry Ghilarov, Konstantin Severinov, Rob Lavigne
Summary: The peptide inhibitor Igy from a Pseudomonas bacteriophage inhibits the gyrase activity and may serve as a potential lead for antibiotic development by targeting the DNA gyrase complex without causing cross-resistance, showing promise in both in vitro and in vivo studies.
Article
Biochemistry & Molecular Biology
Anastasia D. Teplova, Marina V. Serebryakova, Raisa A. Galiullina, Nina V. Chichkova, Andrey B. Vartapetian
Summary: Proteolytic enzymes play crucial roles in plant development, including senescence, through their digestive activity and regulatory functions. By studying the protein partners of plant subtilase phytaspase, it was found to directly interact with endoplasmic reticulum resident calreticulin-3 and cause alterations in its post-translational modification in overproducing plant cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biology
Anastasiia Rusanova, Victor Fedorchuk, Stepan Toshchakov, Svetlana Dubiley, Dmitry Sutormin
Summary: This study provides insights into the metagenomics of three cold-water sponge species from the White Sea, revealing species-specific bacterial and viral communities associated with the sponges. The study also highlights the abundance of virus-host interactions within the sponge-associated community and the occurrence of viral exchanges between communities.
Article
Biochemistry & Molecular Biology
Ekaterina Ilgova, Simon Galkin, Maria Khrenova, Marina Serebryakova, Marina Gottikh, Andrey Anisenko
Summary: This study identified key residues I72, S73, and I76 of Ku70 protein as essential for integrase binding using a peptide fishing assay and site-directed mutagenesis. Molecular dynamics studies revealed a possible mechanism for the interaction between integrase and Ku70. Compounds that inhibit the formation of the integrase complex with Ku70 were identified and confirmed.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Dmitry Bikmetov, Alexander M. J. Hall, Alexei Livenskyi, Bridget Gollan, Stepan Ovchinnikov, Konstantin Gilep, Jenny Y. Kim, Gerald Larrouy-Maumus, Viktor Zgoda, Sergei Borukhov, Konstantin Severinov, Sophie Helaine, Svetlana Dubiley
Summary: This study explores the evolutionary trajectory of GNAT toxins and systematically investigates their substrate specificity using experimental data. The majority of GNAT toxins were found to be specific to Gly-tRNA isoacceptors.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Microbiology
Eldar Yagmurov, Konstantin Gilep, Marina Serebryakova, Yuri Wolf, Svetlana Dubiley, Konstantin Severinov
Summary: In this study, we identified a natural substrate for poorly characterized S51 family proteases from bacteria and showed their contribution to a basal level of resistance to an important class of natural antibiotics. This finding is significant in understanding bacterial resistance mechanisms and developing new strategies against antibiotic resistance.
Article
Biochemical Research Methods
Almasul Alfi, Aleksandr Popov, Ashutosh Kumar, Kam Y. J. Zhang, Svetlana Dubiley, Konstantin Severinov, Shunsuke Tagami
Summary: The study combined rapid cell-free mutant analysis with precise structure prediction to successfully elucidate the structure of difficult-to-purify proteins. A hydrophobic patch on the protein surface was identified as the binding site of its partner protein.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Microbiology
Dmitrii Y. Y. Travin, Romain Jouan, Armelle Vigouroux, Satomi Inaba-Inoue, Joy Lachat, Fazal Haq, Tatiana Timchenko, Dmitry Sutormin, Svetlana Dubiley, Konstantinos Beis, Solange Morera, Konstantin Severinov, Peter Mergaert
Summary: The peptide antibiotic Phazolicin (PHZ) exhibits low resistance in Sinorhizobium meliloti due to its dual-entry mode through two different peptide transporters. This finding makes PHZ an attractive option for the development of biocontrol agents in agriculture.
Review
Biochemistry & Molecular Biology
Dmitrii Y. Travin, Konstantin Severinov, Svetlana Dubiley
Summary: The major obstacle for antimicrobial compounds targeting intracellular processes is entering the cell, some antibiotics use a Trojan horse strategy to mimic specific compounds for the microbe and hijack transport systems to deliver toxic substances. This review summarizes the structures, biosynthesis, and transport mechanisms of natural inhibitors of aminoacyl-tRNA synthetases that rely on this Trojan horse strategy, and presents new data on biosynthetic gene clusters potentially coding for similar inhibitors.
RSC CHEMICAL BIOLOGY
(2021)