A5028802751- Bacteriophages and microbial interactions
- RNA and protein synthesis mechanisms
- Bacterial Genetics and Biotechnology
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- Plant Virus Research Studies
- Advanced biosensing and bioanalysis techniques
- DNA Repair Mechanisms
- Advanced Electron Microscopy Techniques and Applications
- DNA and Biological Computing
- Protein Structure and Dynamics
- RNA Interference and Gene Delivery
- Biochemical and Molecular Research
- Molecular Biology Techniques and Applications
- Modular Robots and Swarm Intelligence
- Monoclonal and Polyclonal Antibodies Research
- RNA Research and Splicing
- Cytomegalovirus and herpesvirus research
- DNA and Nucleic Acid Chemistry
- Evolution and Genetic Dynamics
- Microbial infections and disease research
Peter the Great St. Petersburg Polytechnic University
2014-2024
University Town of Shenzhen
2024
Shenzhen MSU-BIT University
2024
Lomonosov Moscow State University
2024
Institute of Evolutionary Physiology and Biochemistry
2020-2021
National Research University Higher School of Economics
2021
Rutgers, The State University of New Jersey
2015
ABSTRACT Pseudomonas aeruginosa bacteriophage ϕKZ is the type representative of giant phage genus, which characterized by unusually large virions and genomes. By unraveling transcriptional map ∼280-kb genome to single-nucleotide resolution, we combine 369 genes into 134 operons. Early transcription initiated from highly conserved AT-rich promoters distributed across located on same strand genome. does not require or host protein synthesis. Transcription middle late dependent synthesis...
ABSTRACT During infection, the giant phiKZ phage forms a specialized structure at center of host cell called nucleus. This is crucial for safeguarding viral DNA against bacterial nucleases and segregating transcriptional activities late genes. Here, we describe morphological entity, early infection (EPI) vesicle, which appears to be responsible earlier gene segregation beginning process. Using cryo-electron microscopy, electron tomography (ET), fluorescence microscopy with membrane-specific...
The infection of Pseudomonas aeruginosa by the giant bacteriophage phiKZ is resistant to host RNA polymerase (RNAP) inhibitor rifampicin. encodes two sets polypeptides that are distantly related fragments largest subunits cellular multisubunit RNAPs. Polypeptides one set encoded middle phage genes and found in virions. second early absent from Here, we report isolation a five-subunit RNAP phiKZ-infected cells. Four this enzyme homologs non-virion set; fifth subunit protein unknown function....
Abstract During infection, the giant phiKZ phage forms a specialized structure at center of host cell called nucleus. This is crucial for safeguarding viral DNA against bacterial nucleases and segregating transcriptional activities late genes. Here, we describe morphological entity, early infection vesicle (EPI vesicle), which appears to be responsible earlier gene segregation beginning process. Using cryo-electron microscopy, electron tomography, fluorescence microscopy with...
A nucleus-like structure composed of phage-encoded proteins and containing replicating viral DNA is formed in Pseudomonas aeruginosa cells infected by jumbo bacteriophage phiKZ. The PhiKZ genes are transcribed independently from host RNA polymerase (RNAP) two RNAPs encoded the phage. virion RNAP (vRNAP) transcribes early must be injected into cell with phage DNA. non-virion (nvRNAP) gene products late genes. In this work, dynamics localization during phiKZ infection were studied. We provide...
The giant phiKZ phage infection induces the appearance of a pseudo-nucleus inside bacterial cytoplasm. Here, we used RT-PCR, fluorescent in situ hybridization (FISH), electron tomography, and analytical microscopy to study morphology this unique nucleus-like shell demonstrate distribution DNA infected Pseudomonas aeruginosa cells. maturation was traced short intervals for 40 min after revealed continuous spatial separation host DNA. Immediately ejection, located newly-identified round...
Abstract Bacteriophage ΦKZ (PhiKZ) is the archetype of a family massive bacterial viruses. It considered to have therapeutic potential as its host, Pseudomonas aeruginosa, an opportunistic, intrinsically antibiotic resistant, pathogen that kills tens thousands worldwide each year. incredibly interesting virus, expressing many systems host already possesses. On infection, it forms ‘nucleus’, erecting barrier around genome exclude endonucleases and CRISPR-Cas systems. infection independent...
The DprA protein has been implicated in the protection of incoming DNA. However, presence dprA gene family members, also known as smf, across diverse bacterial species suggests a broader functionality for their products. We examined role Escherichia coli DprA/Smf homologue conjugation. Remarkably, Bacillus subtilis dprA/smf can complement an E. mutant, indicating interchangeability genes between competent and non-competent conjugational processes. forms complex with DNA, facilitating...
Bacteriophage ΦKZ (PhiKZ) is the founding member of a family giant bacterial viruses. It has potential as therapeutic its host, Pseudomonas aeruginosa, kills tens thousands people worldwide each year. infection independent host transcriptional apparatus; virus forms "nucleus", producing proteinaceous barrier around genome that excludes immune systems. expresses own non-canonical multi-subunit non-virion RNA polymerase (nvRNAP), which imported into "nucleus" to transcribe viral genes. The...
Abstract A nucleus-like structure composed of phage-encoded proteins and containing replicating viral DNA is formed in Pseudomonas aeruginosa cells infected by jumbo bacteriophage phiKZ. The PhiKZ genes are transcribed independently from host RNA polymerase (RNAP) two RNAPs encoded the phage. virion RNAP (vRNAP) transcribes early must be injected into cell with phage DNA. non-virion (nvRNAP) products late genes. In this work, dynamics localization during phiKZ infection was studied. We...
In this article we study DNA computing, a method which is based on working with molecules in laboratory. That approach implemented solving one of the most popular combinatorial problem — Hamiltonian path problem. Related to recent improvements biophysics methods, are needed for propose change some steps classical algorithm increase accuracy method. The branch-and-bound method, realized computer, also shown paper compare its performance time consumption computing. results that comparison...
Bacteria develop various defense mechanisms against stresses, including the bacteriophage infection. The giant phiKZ phage infection induced appearance of a pseudo-nucleus inside bacterial cytoplasm. Here, we used FISH, electron tomography and analytical microscopy to study morphology this unique nucleus-like shell demonstrate distribution DNA in infected P. aeruginosa cells. maturation was traced short intervals for 40 min after This accompanied by identification real-time RCR. We...
Abstract CrAss-like phages are a recently described family-level group of viruses that includes the most abundant virus in human gut 1,2 . Genomes all crAss-like encode large virion-packaged protein 2,3 contains DFDxD sequence motif, which forms catalytic site cellular multisubunit RNA polymerases (RNAPs) 4 Using Cellulophaga baltica phage phi14:2 as model system, we show this is novel DNA-dependent RNAP translocated into host cell along with DNA and transcribes early genes. We determined...
Abstract In this article different approaches to one of the most popular combinatorial problem — Hamiltonian path – are illustrated and compared between each other. It is shown that it becomes inefficient use branch-and-bound method, method which realized on a computer, from counted number vertices because its exponentially growing complexity, more algorithm based working with deoxyribonucleic acid (DNA) molecules in laboratory analysed. That works parallel has linearly time consumption. Due...
Abstract The DprA protein has been implicated in the protecton of incoming DNA. However, presence dprA gene family members, also known as smf, across diverse bacterial species suggests a broader functonality for their products. We eaamined role Escherichia coli DprA/Smf homologue conjugaton. Remarkably, Bacillus subtilis dprA/smf can complement an E. mutant, indicatng interchangeability genes between competent and non-competent conjugatonal processes. forms complex with DNA, facilitatng...
Antibiotic streptolydigin (Stl) inhibits bacterial transcription by blocking the trigger loop folding in active center of RNA polymerase (RNAP), which is essential for catalysis. We use acoustic force spectroscopy to characterize dynamics elongation ternary complexes (ECs) RNAP presence Stl at a single-molecule level. found that induces long-lived stochastic pauses while instantaneous velocity between unaffected. enhances short-lived associated with an off-pathway early paused state...
Antibiotic streptolydigin (Stl) inhibits bacterial transcription by blocking the trigger loop folding in active center of RNA polymerase (RNAP), which is essential for catalysis. We use acoustic force spectroscopy to characterize dynamics elongation ternary complexes RNAP (ECs) presence Stl at a single-molecule level. found that induces long-lived stochastic pauses while instantaneous velocity between unaffected. enhances short-lived associated with an off-pathway elemental paused state...
Journal Article Helical Reconstruction of the Giant Bacteriophage AR9 tail at Subnanometer Resolution Get access Ilia Sirotkin, Sirotkin Faculty Biology, Lomonosov Moscow State University, Moscow, Russia Search for other works by this author on: Oxford Academic Google Scholar Andrey Moiseenko, Moiseenko RussiaN.N.Semenov Federal Research Center Chemical Physics, Russian Academy Sciences, Daria Antonova, Antonova Peter Great St. Petersburg Polytechnic Petersburg, Maria Yakunina, Yakunina...