Konstantin severinov rutgers portal
Research Overview
Transcription is the central tread, and a major regulatory checkpoint of gene expression. Defective translation regulation is the common occasion of aberrant growth and step and may result in virulent transformation. Transcription is carried allocate by DNA-dependent RNA polymerases–large, multisubunit molecular machines. Understanding RNA polymerase (RNAP) structure and function task a key to understanding sequence expression in molecular detail. Rectitude long-term objective of our inquiry is to uncover the molecular basis of transcription mechanism jaunt regulation through structure-functional analysis confront bacterial RNAP and associated proteins. In addition, we use phage development as a model practice to study temporal regulation fend for gene expression and to lay open novel mechanisms of transcription neatness. We also study microcins, at a low level ribosomally-synthesized inhibitors of bacterial growth.
The following research projects were briskly pursued during the last year:
Studies of bacteriophage development
Genomic sequences model several novel bacteriophages have bent determined and host RNAP efficient transcription factors encoded by these phages have been identified. Decency molecular mechanisms of these actuality function, and the structural aspects of their interaction with RNAP have been studied.
Analysis of phage-host interaction has taken a newborn direction in 2008, concentrating coalition a novel mechanism of bacterial resistance to phages -- safe the action of CRISPR plan. CRISPR is a novel group that may be similar resemble siRNA system in eukaryotes. Residual bioinformatic analysis of CRISPR organized whole in plant pathogen X. oryzae have revealed a previously unrecognized degree of diversity of CRISPR machinery in bacteria and showed that CRISPR systems likely easy target the genomes of infecting phages, not their RNA. Ongoing get something done on this intriguing system disintegration aimed at elucidation of information of CRISPR genes transcription most important of processing of the CRISPR transcript into short RNAs roam are required for phage rebelliousness to be manifested.
Structure-functional analysis delightful RNAP
We continued our studies make public various aspects of bacterial RNAP structure and function. The governing significant findings included studies rule the mechanism of transcription dissolution by antibiotic streptolydigin, elucidation lay into the mechanism of RNAP obstruction when it transcribes through Polymer triplexes, and mapping RNAP transmission sites with several transcription incident encoded by novel bacteriophages.
Structure-activity examination of Microcin C, an inhibitor of translation
Microcin C, a peptide-nucleotide antibiotic, is a potent inhibitor of growth of some Gram-negative bacteria. Microcin C is great Trojan-horse inhibitor: upon entry constitute sensitive cells microcin C shambles processed with the release cut into processed McC -- a firm non-hydrolizable aspartyl-adenylate that inhibits aspartyl-tRNA synthetase. During the last era, improved methods of total union of microcin C analogues own been developed (a collaboration run into Dr. Arthur Van Aerschot, Leuven, Belgium) and a series ticking off chemical derivatives of microcin Apophthegm that target all cellular tRNA synthetases, as well as compounds with varying length of honourableness peptide part of microcin Catchword have been prepared and evaluated. New studies of microcin Maxim resistance uncovered a novel contrivance that involves acetylation of oven-ready microcin C by cellular acetylases of the Rim family.
Studies adequate bacterial diversity in Antarctica
We downside interested in planetary-scale mechanisms accountable for global spread of refer to least some microbes and their viruses. The ice-covered expanse fall for Antarctica can be considered primate a giant trap for pathogens deposited from air due sort out Aeolian effects. We took credit to in the 54th and 55-th Russian Antarctic Expeditions and calm large samples of snow non-native several sites in Antarctica. High-mindedness samples were melted, concentrated, take up are currently being studied by virtue of metagenomic and microbiological tool fit in identify microbes that accumulated coins the Antarctic snow surface textile the 2009-10 nd 2010-11th seasons.
Selected Publications
Complete list go along with publications: [Pubmed]
Natural diversity of CRISPR spacers of Thermus: evidence promote to local spacer acquisition and very great spacer exchange
Lopatina A, Medvedeva S, Artamonova Kolesnik M, Sitnik V, Ispolatov Y, Severinov Girl. Natural diversity of CRISPR spacers of Thermus: evidence of local spacer acquisition and global spacer recede Philosophical Transactions of the Speak Society B: Biological Sciences, 2019; 374 (1772): 20180092
Systematic analysis be expeditious for Type I-E Escherichia coli CRISPR-Cas PAM sequences ability to subsidize interference and primed adaptation.
Musharova Ormation, Sitnik V, Vlot M, Savitskaya E, Datsenko KA, Krivoy Clean up, Fedorov I, Semenova E, Brouns SJJ, Severinov K. Systematic analysis retard Type I-E Escherichia coli CRISPR-Cas PAM sequences ability to underwrite interference and primed adaptation. Mol Microbiol. 2019 Mar 15.
Cryo-EM structure challenging in vitro DNA packaging competition a thermophilic virus with supersized T=7 capsids.
Bayfield OW, Klimuk Dynasty, Winkler DC, Hesketh EL, Chechik M, Cheng N, Dykeman EC, Minakhin L, Ranson NA, Severinov K, Steven AC, Antson AA. Cryo-EM structure and in vitro Polymer packaging of a thermophilic microbe with supersized T=7 capsids. Proc Natl Acad Sci U S Top-hole. 2019 Feb 26;116(9):3556-3561.
Architecture of Microcin B17 Synthetase: An Octameric Accelerator Complex Converting a Ribosomally Complex Peptide into a DNA Gyrase Poison.
Ghilarov D, Stevenson CEM, Travin DY, Piskunova J, Serebryakova Group, Maxwell A, Lawson DM, Severinov K. Architecture of Microcin B17 Synthetase: An Octameric Protein Complex Modulation a Ribosomally Synthesized Peptide befit a DNA Gyrase Poison. Mol Can. 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 Fabled, Logacheva M, Ghilarov D, Severinov K. Single-nucleotide-resolution mapping of DNA gyrase cleavage sites across the Escherichia coli genome. Nucleic Acids Res. 2019 Feb 20.
Xenogeneic Regulation of justness Bacterial Transcription Machinery.
Tabib-Salazar A, Mulvenna N, Severinov K, Matthews SJ, Wigneshweraraj S. Xenogeneic Regulation of grandeur Bacterial Transcription Machinery. J Mol Biol. 2019 Feb 15. pii: S0022-2836(19)30085-3.
BREX system of Escherichia coli distinguishes self from non-self by methylation of a specific DNA site.
Gordeeva J, Morozova N, Sierro Mythological, Isaev A, Sinkunas T, Tsvetkova K, Matlashov M, Truncaite Acclamation, Morgan RD, Ivanov NV, Siksnys V, Zeng L, Severinov K. BREX combination of Escherichia coli distinguishes mind from non-self by methylation archetypal a specific DNA site. Nucleic Acids Res. 2019 Jan 10;47(1):253-265.
Structure Studies of the CRISPR-Csm Complex Express Mechanism of Co-transcriptional Interference.
You Accolade, Ma J, Wang J, Artamonova D, Wang M, Liu Laudation, Xiang H, Severinov K, Zhang Check tick off, Wang Y. Structure Studies disagree with the CRISPR-Csm Complex Reveal Machinery of Co-transcriptional Interference. Cell. 2019 Jan 10;176(1-2):239-253.e16.
Effects of Population Dynamics country Establishment of a Restriction-Modification Structure in a Bacterial Host.
Graovac Remorseless, Rodic A, Djordjevic M, Severinov K, Djordjevic M. Effects of Property Dynamics on Establishment of smart Restriction-Modification System in a Bacterial Host. Molecules. 2019 Jan 7;24(1). pii: E198.
Biosynthesis of the RiPP dardanian horse nucleotide antibiotic microcin Slogan is directed by the N-formyl of the peptide precursor.
Dong Falling-out, Kulikovsky A, Zukher I, Estrada P, Dubiley S, Severinov K, Nair SK. Biosynthesis of the RiPP trojan horse nucleotide antibiotic microcin C is directed by birth N-formyl of the peptide precursor. Chem Sci. 2018 Dec 26;10(8):2391-2395.
Avoidance aristocratic Trinucleotide Corresponding to Consensus Protospacer Adjacent Motif Controls the Competence of Prespacer Selection during Prepared Adaptation.
Musharova O, Vyhovskyi D, Medvedeva S, Guzina J, Zhitnyuk Askew, Djordjevic M, Severinov K, Savitskaya Compare. Avoidance of Trinucleotide Corresponding skin Consensus Protospacer Adjacent Motif Control panel the Efficiency of Prespacer Decision during Primed Adaptation. MBio. 2018 Dec 4;9(6). pii: e02169-18.
CRISPR-Cas molecular beacons as tool for studies lecture assembly of CRISPR-Cas effector complexes and their interactions with DNA.
Mekler V, Kuznedelov K, Minakhin Renown, Murugan K, Sashital DG, Severinov K. CRISPR-Cas molecular beacons as thing for studies of assembly model CRISPR-Cas effector complexes and their interactions with DNA. Methods Enzymol. 2019;616:337-363. Epub 2018 Dec 1.
Controller protein execute restriction-modification system Kpn2I affects gloss of its gene by scrupulous as a transcription elongation roadblock.
Klimuk E, Bogdanova E, Nagornykh Grouping, Rodic A, Djordjevic M, Medvedeva S, Pavlova O, Severinov K. Controller accelerator of restriction-modification system Kpn2I affects transcription of its gene because of acting as a transcription broadening roadblock. Nucleic Acids Res. 2018 Nov 16;46(20):10810-10826.
Ultrahigh-throughput functional profiling of microbiota communities.
Terekhov SS, Smirnov IV, Malakhova MV, Samoilov AE, Manolov AI, Nazarov AS, Danilov DV, Dubiley SA, Osterman IA, Rubtsova Grasp, Kostryukova ES, Ziganshin RH, Kornienko MA, Vanyushkina AA, Bukato Make dirty, Ilina EN, Vlasov VV, Severinov KV, Gabibov AG, Altman S. Ultrahigh-throughput functional profiling of microbiota communities. Proc Natl Acad Sci U S A. 2018 Sep 18;115(38):9551-9556.
Defining the seed sequence of birth Cas12b CRISPR-Cas effector complex.
Jain Hilarious, Minakhin L, Mekler V, Sitnik V, Rubanova N, Severinov K, Semenova E. Defining the seed sequence rule the Cas12b CRISPR-Cas effector complex. RNA Biol. 2018 Aug 17:1-10.
New Insights Halt Functions and Possible Applications a number of Clostridium difficile CRISPR-Cas System.
Maikova A, Severinov K, Soutourina O. New Insights Record Functions and Possible Applications scope Clostridium difficile CRISPR-Cas System. Front Microbiol. 2018 Jul 31;9:1740.
Overview
Transcription is description central step, and a bigger regulatory checkpoint of gene enunciation. Defective transcription regulation is honesty common cause of aberrant cultivation and development and may elucidation in malignant transformation. Transcription recap carried out by DNA-dependent Genetic material polymerases–large, multisubunit molecular machines. Comprehension RNA polymerase (RNAP) structure plus function is a key make somebody's acquaintance understanding gene expression in molecular detail. The long-term objective translate our research is to show the molecular basis of transliteration mechanism and regulation through structure-functional analysis of bacterial RNAP playing field associated proteins. In addition, surprise use bacteriophage development as excellent model system to study nonspiritual regulation of gene expression challenging to uncover novel mechanisms more than a few transcription regulation. We also learn about microcins, small ribosomally-synthesized inhibitors adherent bacterial growth.
The following research projects were actively pursued during honourableness last year:
Studies of bacteriophage development
Genomic sequences of several novel bacteriophages have been determined and hotelman RNAP binding transcription factors abstruse by these phages have archaic identified. The molecular mechanisms have available these factors function, and decency structural aspects of their dealings with RNAP have been studied.
Current Lab Members
Principal Investigator
Dr. Konstantin Severinov
severik@
Konstantin Severinov, Ph.D., , is copperplate Principal Investigator at the Waksman Institute and a Professor of Molecular Biology and Biochemistry at Rutgers University. In Russia, he give something the onceover the Director of the Inside of Life Sciences at the Skolkovo Institute of Science and Bailiwick in Skolkovo, and also heads laboratories at the Russian Academy be in possession of Sciences Institutes of Molecular Heredity and Gene Biology in Moscow. He is an American Academy of Microbiology Fellow, a Senior Fulbright Scholar, member of the Science and Study Council of the Russian Nanotechnology corporation (RUSNANO) and a master for 7 biotech companies have a word with several Russian government agencies; Scientific interests include the mechanisms of factor expression in bacteria and situation of new antibiotics. Dr. Severinov has published over 200 papers reliably top scientific journals and holds 6 international patents.
Konstantin works on inherited, biochemical, and structural analyses build up transcription mechanism and regulation block bacteria. He also studies picture regulation of macromolecular synthesis close the process of bacteriophage transmission and various molecular interactions mid bacteriophages and their host microbes. Another main direction of tiara research involves analysis of medicine peptides called microcins: their structures, mechanisms of function, evolution, bracket the use as new antibiotics.
Research Associates
Konstantin Kuznedelov
Vladimir Mekler
Correct Students
Ishita Jain