Newcastle University

Research Interests

We are investigating transcription. All possible aspects: from mechanisms of reactions to regulation and interactions with other cellular machineries. As a model we are using bacterial RNA polymerases, however most of the results are expandable to archaeas and eukaryots, given an amazing conservation of RNA polymerases in all living organisms. We are using predominantly biochemistry and molecular biology as tools of our studies.

RNA polymerase is one of the most ancient protein enzymes on the planet. Being one of the essential processes in the present day cells, the templated RNA synthesis was the most important processes in RNA and RNA-protein worlds. The main goal of our study is to understand this early day evolution, how RNA polymerase emerged, and evolved to the enzymes we know today.

Interests.
Specific: cellular machineries working with nucleic acids.
General: molecular evolution, physics of high gravities and velocities.

Most recent publications:

Yuzenkova, Y., and Zenkin, N. (2010). Central role of the RNA polymerase trigger loop in intrinsic RNA hydrolysis. Proc Natl Acad Sci U S A.

Yuzenkova, Y., Bochkareva, A., Tadigotla, V.R., Roghanian, M., Zorov, S., Severinov, K., and Zenkin, N. (2010). Stepwise mechanism for transcription fidelity. BMC Biol 8, 54.

• Bochkareva A, Yuzenkova Y, Tadigotla VR, Zenkin N. Factor-independent transcription pausing caused by recognition of the RNA-DNA hybrid sequence. The 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, 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, 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.
• 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.
• 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.