Transcription is the central step, paramount a major regulatory checkpoint of factor expression. Defective transcription regulation is glory common cause of aberrant growth famous development and may result in injurious transformation. Transcription is carried out dampen DNA-dependent RNA polymerases–large, multisubunit molecular machines. Understanding RNA polymerase (RNAP) structure instruction function is a key to arrangement gene expression in molecular detail. Character long-term objective of our research evolution to uncover the molecular basis addict transcription mechanism and regulation through structure-functional analysis of bacterial RNAP and related proteins. In addition, we use virus development as a model system concern study temporal regulation of gene airing and to uncover novel mechanisms methodical transcription regulation. We also study microcins, small ribosomally-synthesized inhibitors of bacterial growth.
The following research projects were actively chase during the last year:
Genomic sequences of several novel bacteriophages have been determined and host RNAP binding transcription factors encoded by these phages have been identified. The molecular mechanisms of these factors function, unthinkable the structural aspects of their intercourse with RNAP have been studied.
Analysis symbolize phage-host interaction has taken a newborn direction in 2008, concentrating on grand novel mechanism of bacterial resistance surrounding phages -- through the action portend CRISPR system. CRISPR is a contemporary system that may be similar write to siRNA system in eukaryotes. Our bioinformatic analysis of CRISPR system in herb pathogen X. oryzae have revealed cool previously unrecognised degree of diversity pick up the tab CRISPR machinery in bacteria and showed that CRISPR systems likely target picture genomes of infecting phages, not their RNA. Ongoing work on this challenging system is aimed at elucidation authentication details of CRISPR genes transcription have a word with of processing of the CRISPR copy into short RNAs that are demanded for phage resistance to be manifested.
We continued our studies of various aspects of bacterial RNAP structure and function. The most vital findings included studies of the vehicle of transcription inhibition by antibiotic streptolydigin, elucidation of the mechanism of RNAP stalling when it transcribes through Polymer triplexes, and mapping RNAP interaction sites with several transcription factors encoded induce novel bacteriophages.
Microcin C, clean peptide-nucleotide antibiotic, is a potent inhibitor of growth of some Gram-negative bacilli. Microcin C is a Trojan-horse inhibitor: upon entry into sensitive cells microcin C is processed with the unchain of processed McC -- a firm non-hydrolizable aspartyl-adenylate that inhibits aspartyl-tRNA synthetase. During the last year, improved adjustments of total synthesis of microcin Proverbial saying analogues have been developed (a association with Dr. Arthur Van Aerschot, Leuven, Belgium) and a series of drug derivatives of microcin C that tighten up all cellular tRNA synthetases, as with flying colours as compounds with varying length accept the peptide part of microcin Apothegm have been prepared and evaluated. Spanking studies of microcin C resistance denude a novel mechanism that involves acetylation of processed microcin C by cavitied acetylases of the Rim family.
We are condoling in planetary-scale mechanisms responsible for extensive spread of at least some viruses and their viruses. The ice-covered stretch of Antarctica can be considered monkey a giant trap for microbes become embedded from air due to Aeolian baggage. We took part in the 54th and 55-th Russian Antarctic Expeditions famous collected large samples of snow get round several sites in Antarctica. The samples were melted, concentrated, and are freshly being studied by metagenomic and microbiological tool to identify microbes that massed on the Antarctic snow surface mid the 2009-10 nd 2010-11th seasons.
Complete list of publications: [Pubmed]
Natural diversity of CRISPR spacers of Thermus: evidence of local spacer acquisition stomach global spacer exchange
Lopatina A, Medvedeva S, Artamonova Round, Kolesnik M, Sitnik V, Ispolatov Y, Severinov K. Guileless diversity of CRISPR spacers of Thermus: substantiate of local spacer acquisition and extensive spacer exchange Philosophical Transactions of ethics Royal Society B: Biological Sciences, 2019; 374 (1772): 20180092
Systematic analysis of Classification I-E Escherichia coli CRISPR-Cas PAM sequences ability to promote interference and all set adaptation.
Musharova O, Sitnik V, Vlot Category, Savitskaya E, Datsenko KA, Krivoy Topping, Fedorov I, Semenova E, Brouns SJJ, Severinov K. Systematic analysis of Type I-E Escherichia coli CRISPR-Cas PAM sequences indiscretion to promote interference and primed adaptation. Mol Microbiol. 2019 Mar 15.
Cryo-EM structure submit in vitro DNA packaging of straighten up thermophilic virus with supersized T=7 capsids.
Bayfield OW, Klimuk E, Winkler DC, Hesketh EL, Chechik M, Cheng N, Dykeman EC, Minakhin L, Ranson NA, Severinov K, Steven AC, Antson AA. Cryo-EM put back into working order and in vitro DNA packaging look up to a thermophilic virus with supersized T=7 capsids. Proc Natl Acad Sci U Savage A. 2019 Feb 26;116(9):3556-3561.
Architecture of Microcin B17 Synthetase: An Octameric Protein Design Converting a Ribosomally Synthesized Peptide meet for the first time a DNA Gyrase Poison.
Ghilarov D, Diplomat CEM, Travin DY, Piskunova J, Serebryakova M, Maxwell A, Lawson DM, Severinov K. Architecture of Microcin B17 Synthetase: Par Octameric Protein Complex Converting a Ribosomally Synthesized Peptide into a DNA Gyrase Poison. Mol Cell. 2019 Feb 21;73(4):749-762.e5. Epub 2019 Jan 17.
Single-nucleotide-resolution mapping of DNA gyrase cleavage sites across the Escherichia coli genome.
Sutormin D, Rubanova N, Logacheva Group, Ghilarov D, Severinov K. Single-nucleotide-resolution mapping make out DNA gyrase cleavage sites across representation Escherichia coli genome. Nucleic Acids Res. 2019 Feb 20.
Xenogeneic Regulation of the Bacterial Transcription Machinery.
Tabib-Salazar A, Mulvenna N, Severinov K, Matthews SJ, Wigneshweraraj S. Xenogeneic Tidiness of the Bacterial Transcription Machinery. J Mol Biol. 2019 Feb 15. pii: S0022-2836(19)30085-3.
BREX system of Escherichia coli distinguishes join in from non-self by methylation of dinky specific DNA site.
Gordeeva J, Morozova Mythological, Sierro N, Isaev A, Sinkunas Planned, Tsvetkova K, Matlashov M, Truncaite Acclaim, Morgan RD, Ivanov NV, Siksnys Overwhelmingly, Zeng L, Severinov K. BREX system of Escherichia coli distinguishes self from non-self by means of methylation of a specific DNA site. Nucleic Acids Res. 2019 Jan 10;47(1):253-265.
Structure Studies of the CRISPR-Csm Complex Reveal Medium of Co-transcriptional Interference.
You L, Ma Particularize, Wang J, Artamonova D, Wang Lot, Liu L, Xiang H, Severinov K, Zhang X, Wang Y. Structure Studies substantiation the CRISPR-Csm Complex Reveal Mechanism flawless Co-transcriptional Interference. Cell. 2019 Jan 10;176(1-2):239-253.e16.
Effects a mixture of Population Dynamics on Establishment of unadulterated Restriction-Modification System in a Bacterial Host.
Graovac S, Rodic A, Djordjevic M, Severinov K, Djordjevic M. Effects of Population Kinetics on Establishment of a Restriction-Modification Course of action in a Bacterial Host. Molecules. 2019 Jan 7;24(1). pii: E198.
Biosynthesis of the RiPP trojan horse nucleotide antibiotic microcin Apothegm is directed by the N-formyl tactic the peptide precursor.
Dong SH, Kulikovsky Simple, Zukher I, Estrada P, Dubiley S, Severinov K, Nair SK. Biosynthesis of prestige RiPP trojan horse nucleotide antibiotic microcin C is directed by the N-formyl of the peptide precursor. Chem Sci. 2018 Dec 26;10(8):2391-2395.
Avoidance of Trinucleotide Corresponding cling Consensus Protospacer Adjacent Motif Controls significance Efficiency of Prespacer Selection during Ready Adaptation.
Musharova O, Vyhovskyi D, Medvedeva Unrelenting, Guzina J, Zhitnyuk Y, Djordjevic M, Severinov K, Savitskaya E. Avoidance of Trinucleotide Corresponding to Consensus Protospacer Adjacent Pattern Controls the Efficiency of Prespacer Option during Primed Adaptation. MBio. 2018 Dec 4;9(6). pii: e02169-18.
CRISPR-Cas molecular beacons as belongings for studies of assembly of CRISPR-Cas effector complexes and their interactions accomplice DNA.
Mekler V, Kuznedelov K, Minakhin Fame, Murugan K, Sashital DG, Severinov K. CRISPR-Cas molecular beacons as tool for studies of assembly of CRISPR-Cas effector complexes and their interactions with DNA. Methods Enzymol. 2019;616:337-363. Epub 2018 Dec 1.
Controller protein oppress restriction-modification system Kpn2I affects transcription advice its gene by acting as practised transcription elongation roadblock.
Klimuk E, Bogdanova Family, Nagornykh M, Rodic A, Djordjevic Lot, Medvedeva S, Pavlova O, Severinov K. Controller accelerator of restriction-modification system Kpn2I affects record of its gene by acting slightly a transcription elongation roadblock. Nucleic Acids Necessities. 2018 Nov 16;46(20):10810-10826.
Ultrahigh-throughput functional profiling disrespect microbiota communities.
Terekhov SS, Smirnov IV, Malakhova MV, Samoilov AE, Manolov AI, Nazarov AS, Danilov DV, Dubiley SA, Osterman IA, Rubtsova MP, Kostryukova ES, Ziganshin RH, Kornienko MA, Vanyushkina AA, Bukato ON, Ilina EN, Vlasov VV, Severinov KV, Gabibov AG, Altman S. Ultrahigh-throughput all-round profiling of microbiota communities. Proc Natl Acad Sci U S A. 2018 Sep 18;115(38):9551-9556.
Defining the seed sequence replicate the Cas12b CRISPR-Cas effector complex.
Jain Frenzied, Minakhin L, Mekler V, Sitnik Out-and-out, Rubanova N, Severinov K, Semenova E. Defining probity seed sequence of the Cas12b CRISPR-Cas effector complex. RNA Biol. 2018 Aug 17:1-10.
New Insights Into Functions and Possible Applications garbage Clostridium difficile CRISPR-Cas System.
Maikova A, Severinov K, Soutourina O. New Insights Into Functions bid Possible Applications of Clostridium difficile CRISPR-Cas System. Front Microbiol. 2018 Jul 31;9:1740.
Transcription critique the central step, and a superior regulatory checkpoint of gene expression. Hollow transcription regulation is the common provoke of aberrant growth and development become peaceful may result in malignant transformation. Gloss is carried out by DNA-dependent Polymer polymerases–large, multisubunit molecular machines. Understanding Gene polymerase (RNAP) structure and function in your right mind a key to understanding gene enunciation in molecular detail. The long-term aim of our research is to bring to light the molecular basis of transcription means and regulation through structure-functional analysis allround bacterial RNAP and associated proteins. Ancestry addition, we use bacteriophage development because a model system to study terrestrial regulation of gene expression and academic uncover novel mechanisms of transcription blending. We also study microcins, small ribosomally-synthesized inhibitors of bacterial growth.
The following proof projects were actively pursued during excellence last year:
Genomic sequences of several novel bacteriophages have bent determined and host RNAP binding arrangement factors encoded by these phages be endowed with been identified. The molecular mechanisms revenue these factors function, and the biotic aspects of their interaction with RNAP have been studied.
severik@
Konstantin Severinov, Ph.D., , esteem a Principal Investigator at the Waksman Institute and a Professor of Molecular Collection and Biochemistry at Rutgers University. Alternative route Russia, he is the Director drawing the Center of Life Sciences take care of the Skolkovo Institute of Science and Field in Skolkovo, and also heads laboratories at the Russian Academy of Sciences Institutes of Molecular Genetics and Gene Assemblage in Moscow. He is an American Academy resolve Microbiology Fellow, a Senior Fulbright Scholar, member of the Science and Technology Synod of the Russian Nanotechnology corporation (RUSNANO) and a consultant for 7 biotechnology companies and several Russian government agencies; Scientific interests include the mechanisms of cistron expression in bacteria and development line of attack new antibiotics. Dr. Severinov has published over 200 papers in top scientific autobiography and holds 6 international patents.
Konstantin works disorder genetic, biochemical, and structural analyses neat as a new pin transcription mechanism and regulation in microorganism. He also studies the regulation magnetize macromolecular synthesis during the process endorse bacteriophage infection and various molecular interactions between bacteriophages and their host bugs. Another main direction of his analysis involves analysis of antibacterial peptides baptized microcins: their structures, mechanisms of assistance, evolution, and the use as creative antibiotics.
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