Background

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Research

 

 Research interests

My research focuses on transcription, the first stage of gene expression and a major point of the regulation of cellular processes.

Under this main theme my group’s current research directions are:

non-canonical RNA capping with metabolic cofactors and cell wall precursors;

transcription in cyanobacteria and plastids (chloroplast and apicoplast, relic non-green chloroplast);

circadian clocking of gene expression and its applications for synthetic biology;

antibiotics and viral inhibitors of bacterial transcription.

Publications

• Articles

  • Qayyum MZ, Imashimizu M, Leanca M, Vishwakarma RK, Riaz-Bradley A, Yuzenkova Y, Murakami KS. Structure and function of the Si3 insertion integrated into the trigger loop/helix of cyanobacterial RNA polymerase. Proceedings of the National Academy of Sciences of the United States of America 2024, 121(8), e2311480121.
  • Shen L, Lai G, You L, Shi J, Wu X, Puiu M, Gu Z, Feng Y, Yuzenkova Y, Zhang Y. An SI3-σ arch stabilizes cyanobacteria transcription initiation complex. Proceedings of the National Academy of Sciences of the United States of America 2023, 120(16), e2219290120.
  • Julius C, Salgado PS, Yuzenkova Y. Metabolic cofactors NADH and FAD act as non-canonical initiating substrates for a primase and affect replication primer processing in vitro. Nucleic Acid Research 2020, 48(13), 7298-7306.
  • Riaz-Bradley A, James K, Yuzenkova Y. High intrinsic hydrolytic activity of cyanobacterial RNA polymerase compensates for the absence of transcription proofreading factors. Nucleic Acids Research 2020, 48(3), 1341-1352.
  • Julius C, Riaz-Bradley A, Yuzenkova Y. RNA capping by mitochondrial and multi-subunit RNA polymerases. Transcription 2018, 9(5), 292-297.
  • Mosaei H, Molodtsov V, Kepplinger B, Harbottle J, Moon C, Jeeves R, Ceccaroni L, Shin Y, Morton-Laing S, Marrs ECL, Wills C, Clegg W, Yuzenkova J, Perry JD, Bacon J, Errington J, Allenby NEE, Hall MJ, Murakami KS, Zenkin N. Mode of Action of Kanglemycin A, an Ansamycin Natural Product that Is Active against Rifampicin Resistant Mycobacterium tuberculosis. Molecular Cell 2018, 72(2), 263-274.
  • Forrest D, James K, Yuzenkova Y, Zenkin N. Single-peptide DNA-dependent RNA polymerase homologous to multi-subunit RNA polymerase. Nature Communications 2017, 8, 15774.
  • Julius C, Yuzenkova Y. Bacterial RNA polymerase caps RNA with various cofactors and cell wall precursors. Nucleic Acids Research 2017, 45(14), 8282-8290.
  • van Nues RW, Castro-Roa D, Yuzenkova Y, Zenkin N. Ribonucleoprotein particles of bacterial small non-coding RNA IsrA (IS61 or McaS) and its interaction with RNA polymerase core may link transcription to mRNA fate. Nucleic Acids Research 2016, 44(6), 2577-2592.
  • Zenkin N, Yuzenkova Y. New Insights into the Functions of Transcription Factors that Bind the RNA Polymerase Secondary Channel. Biomolecules 2015, 25(3), 1195-1209.
  • Zenkin N, Severinov K, Yuzenkova Y. Bacteriophage Xp10 anti-termination factor p7 induces forward translocation by host RNA polymerase. Nucleic Acids Research 2015, 43(13), 6299-6308.
  • Roghanian M, Zenkin N, Yuzenkova Y. Bacterial global regulators DksA/ppGpp increase fidelity of transcription. Nucleic Acids Research 2015, 43(3), 1529-1536.
  • Sustarsic M, Plochowietz A, Aigrain L, Yuzenkova Y, Zenkin N, Kapanidis A. Optimized delivery of fluorescently labeled proteins in live bacteria using electroporation. Histochemistry and Cell Biology 2014, 142(1), 113-124.
  • Yuzenkova Y, Gamba P, Herber M, Attaiech L, Shafeeq S, Kuipers OP, Klumpp S, Zenkin N, Veening JW. Control of transcription elongation by GreA determines rate of gene expression in Streptococcus pneumoniae. Nucleic Acids Research 2014, 42(17), 10987-10999.
  • Zorov S, Yuzenkova Y, Nikiforov V, Severinov K, Zenkin N. Antibiotic streptolydigin requires non-catalytic Mg²⁺ for binding to RNA polymerase. Antimicrobial Agents and Chemotherapy 2014, 58(3), 1420-1424.
  • Yuzenkova Y, Roghanian M, Bochkareva A, Zenkin N. Tagetitoxin inhibits transcription by stabilizing pre-translocated state of the elongation complex. Nucleic Acids Research 2013, 41(20), 9257-9265.
  • Nielsen S, Yuzenkova Y, Zenkin N. Mechanism of Eukaryotic RNA Polymerase III Transcription Termination. Science 2013, 340(6140), 1577-1580.
  • Yuzenkova Y, Roghanian M, Zenkin N. Multiple active centers of multi-subunit RNA polymerases. Transcription 2012, 3, 115-118.
  • Bochkareva A, Yuzenkova Y, Tadigotla VR, Zenkin N. Factor-independent transcription pausing caused by recognition of the RNA-DNA hybrid sequence. EMBO Journal 2012, 31(3), 630-639.
  • Roghanian M, Yuzenkova Y, Zenkin N. Controlled interplay between trigger loop and Gre factor in the RNA polymerase active centre. Nucleic Acids Research 2011, 39(10), 4352-4359.
  • Yuzenkova Y, Tadigotla VR, Severinov K, Zenkin N. A new basal promoter element recognized by RNA polymerase core enzyme. EMBO Journal 2011, 30(18), 3766-3775.
  • Yuzenkova Y, Bochkareva A, Tadigotla VR, Roghanian M, Zorov S, Severinov K, Zenkin N. Stepwise mechanism for transcription fidelity. BMC Biology 2010, 8(1), 54.
  • Yuzenkova Y, Zenkin N. Central role of the RNA polymerase trigger loop in intrinsic RNA hydrolysis. Proceedings of the National Academy of Sciences 2010, 107(24), 10878-10883.
  • Yuzenkova Y, Zenkin N, Severinov K. Mapping of RNA Polymerase Residues that Interact with Bacteriophage Xp10 Transcription Antitermination Factor p7. Journal of Molecular Biology 2008, 375(1), 29-35.
  • Zenkin N, Kulbachinskiy A, Yuzenkova Y, Mustaev A, Bass I, Severinov K, Brodolin K. Region 1.2 of the RNA polymerase sigma subunit controls recognition of the -10 promoter element. EMBO Journal 2007, 26(4), 955-964.
  • Zenkin N, Yuzenkova Y, Severinov K. Transcript-Assisted Transcriptional Proofreading. Science 2006, 313(5786), 518-520.
  • deCristóbal RE, Solbiati JO, Zenoff AM, Vincent PA, Salomón RA, Yuzenkova J, Severinov K, Farías RN. Microcin J25 uptake: His5 of the MccJ25 lariat ring is involved in interaction with the inner membrane MccJ25 transporter protein SbmA. J Bacteriol 2006, 188(9):3324-8.
  • Semenova E, Yuzenkova Y, Peduzzi J, Rebuffat S, Severinov K. Structure-activity analysis of microcinJ25: distinct parts of the threaded lasso molecule are responsible for interaction with bacterial RNA polymerase. J Bacteriol 2005, 187(11):3859-63.
  • Adelman K, Yuzenkova J, LaPorta A, Zenkin N, Lee J, Lis JT, Borukhov S, Wang MD, Severinov K. Molecular mechanism of transcription inhibition by peptide antibiotic Microcin J25. Mol Cell 2004, 14, 753-62.
  • Wilson KA, Kalkum M, Ottesen J, Yuzenkova J, Chait BT, Landick R, Muir T, Severinov K, Darst SA. Structure of microcin J25, a peptide inhibitor of bacterial RNA polymerase, is a lassoed tail. J Am Chem Soc 2003, 125(41):12475-83.
  • Yuzenkova J, Nechaev S, Berlin J, Rogulja D, Kuznedelov K, Inman R, Mushegian A, Severinov K. Genome of Xanthomonas oryzae bacteriophage Xp10: an odd T-odd phage. J Mol Biol 2003, 330(4):735-48.
  • Yuzenkova J, Delgado M, Nechaev S, Savalia D, Epshtein V, Artsimovitch I, Mooney RA, Landick R, Farias RN, Salomon R, Severinov K. Mutations of bacterial RNA polymerase leading to resistance to microcin j25. J Biol Chem 2002, 277(52):50867-75.
  • Nechaev S, Yuzenkova Y, Niedziela-Majka A, Heyduk T, Severinov K. A novel bacteriophage-encoded RNA polymerase binding protein inhibits transcription initiation and abolishes transcription termination by host RNA polymerase. J Mol Biol 2002.

• Editorial

  • Nielsen S, Zenkin N. Response to Comment on "Mechanism of eukaryotic RNA polymerase III transcription termination". Science 2014, 345(6196), 524-524.

• Reviews

  • Wiedermannova J, Julius C, Yuzenkova Y. The expanding field of non-canonical RNA capping: New enzymes and mechanisms. Royal Society Open Science 2021, 8(5).
  • Julius C, Yuzenkova Y. Noncanonical RNA-capping: Discovery, mechanism, and physiological role debate. Wiley Interdisciplinary Reviews: RNA 2019, 10(2), e1512.