Professor Nikolay Zenkin
Professor of Molecular Biology
- Email: firstname.lastname@example.org
- Telephone: +44 (0) 191 208 3227
- Fax: +44 (0) 191 208 7424
- Address: The Centre for Bacterial Cell Biology
Medical Science New Building
Newcastle upon Tyne
Molecular basis of gene expression
Transcription, copying genetic information into RNA, is the first step of gene expression. In all living organisms transcription is accomplished by conserved multi-subunit RNA polymerases, one of the most ancient enzymes on the planet. Understanding functions of RNA polymerase are essential for understanding evolution of Life of the planet. Importantly, malfunctions of RNA polymerases are linked to various human diseases including cancer and Alzheimer. Also transcription is the potent target for antimicrobials. Many mechanistic details of the functioning of RNA polymerases are not clear. Furthermore RNA polymerases are imbedded in intricate relations with other cellular machineries, such as translation in prokaryotes or replication and repair in all organisms. Regulation of these interactions is pivotal for coordination of cellular processes, correct gene expression and ultimately for survival of organisms. The mechanisms underlining these interactions and their regulation are also poorly understood.
We are investigating transcription. All possible aspects: from mechanisms of reactions and inhibition by antibiotics to regulation and interactions with other cellular machineries, such as translation and replication. We use classical biochemistry and molecular biology, some unique experimental systems as well as novel techniques. In vitro we investigate bacterial and archaeal RNA polymerases as well as eukaryotic RNA polymerases I, II and III. In vivo we are focusing on bacterial transcription.
The main goal of our study is to understand how RNA polymerase evolved to the enzyme we know today, and how it functions and is regulated in the modern cells. Another important aspect of our work is to look for the ways of manipulation of RNA polymerases (such as specific inhibition) in order to control pathogenicity.
Bacterial defence systems
Bacteria invented several mechanisms to fight against their enemies –bacteriophages and antibiotics. One of such systems, toxin-antitoxin (TA) systems, involves a large number of small proteins, called toxins, which reversibly target essential processes in the bacterial cell to stop these processes and bring the cell to dormancy. Such dormant cells become temporarily resistant to antibiotics (phenomenon called persistence) because antibiotic targets are temporarily non-functional in them, as well as become “not interesting” to bacteriophages, because they cannot propagate in dormant cells. There are also some other biological important phenomena, such as programmed cell death and addiction to plasmids, linked to TA systems. TA systems involve large number of activities and targets, many of which are not yet known or characterised.
We are interested in mechanistic and catalytic details of functioning of TAs and the outcomes of their action for their targets.
Toxin-antitoxin system described above is a “passive” one, i.e. the cell uses it to wait through the harsh conditions. Recently an “active” defensive immune system of bacteria (CAS/CRISPR system) was discovered. Bacteria store information about bacteriophages that have attacked them in the past, and use this information to kill bacteriophages if they enter the cell again. Bacterial immune system, however, is not related to the known immune systems. Information about the phage is stored in bacterial genome as short sequences (called CRISPRs) complementary to the phage genome. Upon phage invasion, the sequences are transcribed and the processed RNA along with large protein complex (CAS proteins) recognises phage genome and/or phage mRNA and destroys it.
The process of phage recognition and destruction is well studied. We are interested in the mechanism of acquisition of the immunity memory by CAS/CRISPR system, which remain a mystery.
Specific: cellular machineries working with nucleic acids.
General: molecular evolution, physics of high gravities and velocities.
1. Castro-Roa, D., Garcia-Pino, A, van Nuland, N. A. J., Loris, R., and Zenkin, N*. (2013) The Fic protein Doc uses an inverted substrate to phosphorylate and inactivate EF-Tu. Nat Chem Biol 9:811-7
2. Germain, E., Daniel Castro-Roa, D., Zenkin, N*., and Gerdes, K. (2013) Molecular Mechanism of Bacterial Persistence by HipA. Mol Cell 52:248-54
3. Nielsen, S.U., Yuzenkova, Y., and Zenkin, N*. (2013). Mechanism of RNA polymerase III transcription termination Science, 340: 1577-1580.
4. Bochkareva, A., Yuzenkova, Y., Tadigotla, V. and Zenkin, N*. (2012). Factor-independent transcription pausing caused by recognition of the RNA-DNA hybrid sequence. EMBO J 31, 630-639
5. Yuzenkova, Y., Tadigotla, V.R., Severinov, K., and Zenkin, N*. (2011). A new basal promoter element recognized by RNA polymerase core enzyme. EMBO J 30, 3766-3775.
6. Yuzenkova, Y., Zenkin, N*. (2010) Central role of the RNA polymerase trigger loop in intrinsic RNA hydrolysis Proc Natl Acad Sci U S A 107(24):10878-83
7. Zenkin, N., Kulbachinskiy, A., Yuzenkova, Y., Mustaev, A., Bass, I., Severinov, K. and Brodolin, K. (2007). Region 1.2 of the RNA polymerase sigma subunit controls recognition of the -10 promoter element. EMBO J 26, 955-64.
8. Zenkin, N*., Yuzenkova, Y. and Severinov, K. (2006) Transcript-assisted transcriptional proofreading. Science, 313, 518-20.
9. Zenkin, N*., Naryshkina, T., Kuznedelov, K. and Severinov, K. (2006) The mechanism of DNA primer synthesis by RNA polymerase. Nature, 439, 617
- Gamba P, Zenkin N. Transcription fidelity and its roles in the cell. Current Opinion in Microbiology 2018, 42, 13-18.
- Gamba P, James K, Zenkin N. A link between transcription fidelity and pausing in vivo. Transcription 2017, 8(2), 99-105.
- James K, Cockell SJ, Zenkin N. Deep sequencing approaches for the analysis of prokaryotic transcriptional boundaries and dynamics. Methods 2017, 120, 76-84.
- James K, Gamba P, Cockell SJ, Zenkin N. Misincorporation by RNA polymerase is a major source of transcription pausing in vivo. Nucleic Acids Research 2017, 45(3), 1105-1113.
- 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.
- Tyler A, Sejzi HM, Morton S, Waddell PG, Wills C, McFarlane W, Gray J, Goodfellow M, Errington J, Allenby N, Zenkin N, Hall MJ. Structural Reassignment and Absolute Stereochemistry of Madurastatin C1 (MBJ-0034) and the Related Aziridine Siderophores: Madurastatins A1, B1 and MBJ-0035. Journal of Natural Products 2017, 80(5), 1558–1562.
- Roghanian M, Zenkin N, Yuzenkova Y. Bacterial global regulators DksA/ppGpp increase fidelity of transcription. Nucleic Acids Research 2015, 43(3), 1529-1536.
- 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.
- Castro-Roa D, Zenkin N. Methodology for the analysis of transcription and translation in transcription-coupled-to-translation systems in vitro. Methods 2015, 86, 51-59.
- Castro-Roa D, Zenkin N. Methods for the Assembly and Analysis of In Vitro Transcription-Coupled-to-Translation Systems. In: Irina Artsimovitch and Thomas J. Santangelo, ed. Bacterial Transcriptional Control. New York, NY. USA: Springer New York, 2015, pp.81-99.
- 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.
- 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 2015, epub ahead of print.
- Zenkin N. Ancient RNA stems that terminate transcription. RNA Biology 2014, 11(4), 295-297.
- 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, 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.
- Zenkin N. Multiple personalities of the RNA polymerase active centre. Microbiology 2014, 160, 1316-1320.
- 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.
- Zenkin N. RNA secondary structure-dependent termination of transcription. Cell Cycle 2014, 13, 3-4.
- Garcia-Pino A, Zenkin N, Loris R. The many faces of Fic: structural and functional aspects of Fic enzymes. Trends in Biochemical Sciences 2014, 39(3), 121-129.
- Nielsen S, Yuzenkova Y, Zenkin N. Mechanism of Eukaryotic RNA Polymerase III Transcription Termination. Science 2013, 340(6140), 1577-1580.
- Kuzmenko A, Atkinson GC, Levitskii S, Zenkin N, Tenson T, Hauryliuk V, Kamenski P. Mitochondrial translation initiation machinery: Conservation and diversification. Biochimie 2013, 100, 132-140.
- Germain E, Castro-Roa D, Zenkin N, Gerdes K. Molecular Mechanism of Bacterial Persistence by HipA. Molecular Cell 2013, 52(2), 248-254.
- Kuzmenko AV, Levitskii SA, Vinogradova EN, Atkinson GC, Hauryliuk V, Zenkin N, Kamenski PA. Protein biosynthesis in mitochondria. Biochemistry (Moscow) 2013, 78(8), 855-866.
- 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.
- Castro-Roa D, Garcia-Pino A, De Geiter S, van Nuland NAJ, Loris R, Zenkin N. The Fic protein Doc uses an inverted substrate to phosphorylate and inactivate EF-Tu. Nature Chemical Biology 2013, 9(12), 811-817.
- Castro-Roa D, Garcia-Pino A, De Gieter S, van Nuland NAJ, Loris R, Zenkin N. The Fic protein Doc uses an inverted substrate to phosphorylate and inactivate EF-Tu. Nature Chemical Biology 2013, 9(12), 811-817.
- Bochkareva A, Zenkin N. The sigma70 region 1.2 regulates promoter escape by unwinding DNA downstream of the transcription start site. Nucleic Acids Research 2013, 41(8), 4565-4572.
- Nielsen S, Zenkin N. Transcript assisted phosphodiester bond hydrolysis by eukaryotic RNA polymerase II. Transcription 2013, 4(5), 209-212.
- 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.
- Zenkin N. Hypothesis: Emergence of Translation as a Result of RNA Helicase Evolution. Journal of Molecular Evolution 2012, 74(5-6), 249-256.
- Castro-Roa D, Zenkin N. In vitro experimental system for analysis of transcription-translation coupling. Nucleic Acids Research 2012, 40(6), e45.
- Yuzenkova Y, Roghanian M, Zenkin N. Multiple active centers of multi-subunit RNA polymerases. Transcription 2012, 3, 115-118.
- 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.
- 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.
- Castro-Roa D, Zenkin N. Relations Between Replication and Transcription . In: Kušić-Tišma, J, ed. Fundamental Aspects of DNA Replication. Rijeka, Croatia: InTech Open, 2011, pp.289-306.
- 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, 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, 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, Severinov K. RNA polymerase - The third class of primases. Cellular and Molecular Life Sciences 2008, 65(15), 2280-2288.
- 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, Naryshkina T, Kuznedelov K, Severinov K. The mechanism of DNA replication primer synthesis by RNA polymerase. Nature 2006, 439(7076), 617-620.
- Zenkin N, Yuzenkova Y, Severinov K. Transcript-Assisted Transcriptional Proofreading. Science 2006, 313(5786), 518-520.
- Zenkin N, Kulbachinskiy A, Bass I, Nikiforov V. Different rifampin sensitivities of Escherichia coli and Mycobacterium tuberculosis RNA polymerases are not explained by the difference in the beta-subunit rifampin regions I and II. Antimicrob Agents Chemother 2005, 49, 1587-90.
- Brodolin K, Zenkin N, Severinov K. Remodeling of the sigma70 subunit non-template DNA strand contacts during the final step of transcription initiation. J Mol Biol 2005, 350, 930-7.
- Temiakov D, Zenkin N, Vassylyeva MN, Perederina A, Tahirov TH, Kashkina E, Savkina M, Zorov S, Nikiforov V, Igarashi N, Matsugaki N, Wakatsuki S, Severinov K, Vassylyev DG. Structural Basis of Transcription Inhibition by Antibiotic Streptolydigin. Molecular Cell 2005, 19(5), 655-666.
- Campbell EA, Pavlova O, Zenkin N, Leon F, Irschik H, Jansen R, Severinov K, Darst SA. Structural, functional, and genetic analysis of sorangicin inhibition of bacterial RNA polymerase. EMBO J 2005, 24, 674-82.
- Budarina ZI, Nikitin DV, Zenkin N, Zakharova M, Semenova E, Shlyapnikov MG, Rodikova EA, Masyukova S, Ogarkov O, Baida GE, Solonin AS, Severinov K. A new Bacillus cereus DNA-binding protein, HlyIIR, negatively regulates expression of Bcereus haemolysin II. Microbiology 2004, 150, 3691-701.
- 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.
- Wigneshweraraj SR, Burrows PC, Nechaev S, Zenkin N, Severinov K, Buck M. Regulated communication between the upstream face of RNA polymerase and the beta subunit jaw domain. EMBO J 2004, 23, 4264-74.
- Zenkin N, Severinov K. The role of RNA polymerase σ subunit in promoter-independent initiation of transcription. Proceedings of the National Academy of Sciences of the United States of America 2004, 101(13), 4396-4400.
- Brodolin K, Zenkin N, Mustaev A, Mamaeva D, Heumann H. The sigma 70 subunit of RNA polymerase induces lacUV5 promoter-proximal pausing of transcription. Nat Struct Mol Biol 2004, 11, 551-7.