Pupov Danil Vladimirovich | Institute of Molecular Genetics

Pupov Danil Vladimirovich

Academic degree:
Doctor of Philosophy (Biology)

Academic title:
without academic rank

Division of IMG:
Laboratory of molecular genetics of microorganisms

Senior Researcher


Resume (CV):

Main research interests

My current research is focused on studies of molecular mechanisms of transcription in bacteria, including analysis of transcription regulation by DNA and RNA-encoded signals, protein transcription factors and small molecules. I also develop novel types of promoter substrates and RNA polymerase inhibitors based on highly specific aptamer ligands to bacterial RNA polymerase.
My recent projects include:
1) investigation of the mechanisms of action of different transcription inhibitors, including rifampicin;
2) selection of aptamers to different epitopes of bacterial RNAP;
3) analysis of the mechanisms of nucleotide selection by RNAP;
4) analysis of general principles of transcription on single-stranded templates;
5) investigation of the roles of different regions of the sigma subunit in transcription initiation;
6) analysis of the roles of conserved DNA-interacting regions of RNAP at various stages of transcription.

Teaching activities

Supervisor of 7 diploma students, 7 defended diploma theses.

Awards, achievements, memberships

  1. Medal of Russian Academy of Science for young scientists (2016)
  2. Stipend of the “Future of Molecular Genetics” Foundation (2010, 2012, 2014)
  3. Member of the Russian Biochemical Society (2010)
  4. Member of the Biochemical Society (United Kingdom) (2010)


  1. Oguienko A., Petushkov I., Pupov D., Esyunina D., Kulbachinskiy A. 2021. Universal functions of the σ finger in alternative σ factors during transcription initiation by bacterial RNA polymerase. RNA biology. Feb 25;1-10. Online ahead of print. IF 2019: 5,350. Quartiles: Q1. Citations 2021: 0. https://doi.org/10.1080/15476286.2021.1889254
  2. Shin Y., Qayyum M.Z., Pupov D., Esyunina D., Kulbachinskiy A., Murakami K.S. 2021. Structural basis of ribosomal RNA transcription regulation. Nature communications. Jan 22;12(1):528. IF 2020: 14,919. Quartiles: Q1. Citations 2021: 6. https://doi.org/10.1038/s41467-020-20776-y
  3. Pletnev P., Pupov D., Pshanichnaya L., Esyunina D., Petushkov I., Nesterchuk M., Osterman I., Rubtsova M., Mardanov A., Ravin N., Sergiev P., Kulbachinskiy A., Dontsova O. 2020. Rewiring of growth-dependent transcription regulation by a point mutation in region 1.1 of the housekeeping σ factor. Nucleic acids research. Nov 4;48(19):10802-10819. IF 2020: 16,971. Quartiles: Q1. Citations 2021: 1. https://doi.org/10.1093/nar/gkaa798
  4. Shikalov AB, Esyunina DM, Pupov DV, Kulbachinskiy AV, Petushkov IV. 2019. The σ24 Subunit of Escherichia coli RNA Polymerase Can Induce Transcriptional Pausing in vitro. Biochemistry (Moscow). 84(4):426-434. IF 2020: 2,487. Quartiles: Q2. Citations 2021: 1. https://doi.org/10.1134/s0006297919040102
  5. Pupov D., Ignatov A., Agapov A., Kulbachinskiy A. 2019. Distinct effects of DNA lesions on RNA synthesis by Escherichia coli RNA polymerase. Biochemical and biophysical research communications. 510:122-127. IF 2020: 3,575. Quartiles: Q2. Citations 2021: 6. https://doi.org/10.1016/j.bbrc.2019.01.062
  6. Esyunina D., Pupov D., Kulbachinskiy A. 2019. Dual role of the σ factor in primer RNA synthesis by bacterial RNA polymerase. FEBS letters. 593:361-368. IF 2020: 4,124. Quartiles: Q1. Citations 2021: 0. https://doi.org/10.1002/1873-3468.13312
  7. Pupov D., Petushkov I., Esyunina D., Murakami K.S., Kulbachinskiy A. 2018. Region 3.2 of the σ factor controls the stability of rRNA promoter complexes and potentiates their repression by DksA. Nucleic acids research. 46:11477-11487. IF 2020: 16,971. Quartiles: Q1. Citations 2021: 11. https://doi.org/10.1093/nar/gky919
  8. Petushkov I., Esyunina D., Mekler V., Severinov K., Pupov D., Kulbachinskiy A. 2017. Interplay between σ region 3.2 and secondary channel factors during promoter escape by bacterial RNA polymerase. Biochemical journal. 474: 4053–4064. IF 2019: 4,097. Quartiles: Q1. Citations 2021: 12. https://doi.org/10.1042/bcj20170436
  9. Agapov A., Esyunina D., Pupov D., Kulbachinskiy A. 2016. Regulation of transcription initiation by Gfh factors from Deinococcus radiodurans. Biochemical journal. 473(23):4493-4505. IF 2019: 4,097. Quartiles: Q1. Citations 2021: 6. https://doi.org/10.1042/bcj20160659
  10. Esyunina D., Turtola M., Pupov D., Bass I., Klimašauskas S., Belogurov G., Kulbachinskiy A. 2016. Lineage-specific variations in the trigger loop modulate RNA proofreading by bacterial RNA polymerases. Nucleic acids research. 44:1298-1308. IF 2020: 16,971. Quartiles: Q1. Citations 2021: 21. https://doi.org/10.1093/nar/gkv1521
  11. Petushkov I., Pupov D., Bass I., Kulbachinsky A. 2015. Mutations in the CRE pocket of bacterial RNA polymerase affect multiple steps of transcription. Nucleic acids research. 43:5798-5809. IF 2020: 16,971. Quartiles: Q1. Citations 2021: 17. https://doi.org/10.1093/nar/gkv504
  12. Pupov D., Kulbachinskiy A. 2015. Single-stranded DNA aptamers for functional probing of bacterial RNA polymerase. Methods in Molecular Biology. 1276:165-83. IF 2020: 1,17. Quartiles: Q3. Citations 2021: 1. https://doi.org/10.1007/978-1-4939-2392-2_9
  13. Basu R.S., Warner B.S., Molodtsov V., Pupov D., Esyunina D., Fernandez-Tornero C., Kulbachinskiy A., Murakami K.S. 2014. Structural basis of transcription initiation by bacterial RNA polymerase holoenzyme. Journal of biological chemistry. 289, 24549-24559. IF 2020: 5,157. Quartiles: Q1. Citations 2021: 119. https://doi.org/10.1074/jbc.m114.584037
  14. Pupov D., Kuzin I.A., Bass I., Kulbachinskiy A. 2014. Distinct functions of the RNA polymerase σ subunit region 3.2 in RNA priming and promoter escape. Nucleic acids research. 42:4494-4504. IF 2020: 16,971. Quartiles: Q1. Citations 2021: 55. https://doi.org/10.1093/nar/gkt1384
  15. Pupov D., Esyunina D., Feklistov A. and Kulbachinskiy A. 2013. Single-strand promoter traps for bacterial RNA polymerase. Biochemical journal. 452(2): 241-248. IF 2019: 4,097. Quartiles: Q1. Citations 2021: 5. https://doi.org/10.1042/bj20130069
  16. Miropolskaya N., Ignatov A., Bass I., Zhilina E., Pupov D., Kulbachinskiy A. 2012. Distinct functions of regions 1.1 and 1.2 of RNA polymerase σ subunits from Escherichia coli and Thermus aquaticus in transcription initiation. Journal of biological chemistry. 287: 23779-23789. IF 2020: 5,157. Quartiles: Q1. Citations 2021: 10. https://doi.org/10.1074/jbc.m112.363242
  17. Pupov D., Miropolskaya N., Sevostyanova A., Bass I., Artsimovitch I., Kulbachinskiy A. 2010. Multiple roles of the RNA polymerase β′-SW2 region in transcription initiation, promoter escape, and RNA elongation. Nucleic acids research. 38: 5784-5796. IF 2020: 16,971. Quartiles: Q1. Citations 2021: 31. https://doi.org/10.1093/nar/gkq355
  18. Pupov D.V., Kulbachinskiy A.V. 2010. Structural dynamics of the active center of multisubunit RNA polymerases during RNA synthesis and proofreading. Review. Molekulyarnaya Biologiya. 44: 573-590. IF 2020: 0,492. Quartiles: Q4. Citations 2021: 3. https://www.elibrary.ru/item.asp?id=15331031
  19. Pupov D.V., Barinova N.A., Kulbachinskiy A.V. 2008. Analysis of RNA Cleavage by RNA Polymerases from Escherichia coli and Deinococcus radiodurans. Biochemistry (Moscow), 73:725-729. IF 2020: 2,487. Quartiles: Q2. Citations 2021: 9. https://doi.org/10.1134/s000629790806014x
  20. Mozhina N.V., Burmistrova O.A., Pupov D.V., Rudenskaya G.N., Dunaevsky Ya.E., Demiduk I.V., and Kostrov S.V. 2008. Isolation and properties of Serratia proteamaculans 94 Cysteine Protease. Russian Journal of Bioorganic Chemistry. 34(3):303-9. IF 2020: 0,79. Quartiles: Q4. Citations 2021: 8. https://doi.org/10.1134/s1068162008030035
  21. Rudenskaya G.N., Pupov D.V. 2008. Cysteine proteinases of microorganisms and viruses. Review. Biochemistry (Moscow). 73(1):1-13. IF 2020: 2,487. Quartiles: Q2. Citations 2021: 27. https://doi.org/10.1134/s000629790801001x