Kulbachinskiy Andrey Vladimirovich | Institute of Molecular Genetics

Kulbachinskiy Andrey Vladimirovich

Academic degree:
Doctor of Biological Sciences

Academic title:
without academic rank


Division of IMG:
Laboratory of molecular genetics of microorganisms
Laboratory of RNA biology and epigenetics

Position:
Head of Laboratory


Telephone:
+7-499-196-00-15

Е-mail:
akulb@img.ras.ru



Main research interests

Molecular mechanisms of transcription, RNA polymerase structure and function, DNA repair and horizontal gene transfer in bacteria.
 
The main research directions include:
(1) Analysis of the molecular mechanisms of transcription in diverse bacteria.
(2) Structure-based studies of the catalytic mechanisms of bacterial RNA polymerase.
(3) Analysis of the mechanisms of transcription pausing and termination and regulation of these processes by bacterial and phage-encoded factors.
(4) Characterization of highly specific aptamers to bacterial RNA polymerase and transcription factors.
(5) Analysis of the interplay between transcription and other genetic processes, including DNA replication and repair.
(6) Analysis of horizontal gene transfer and its regulation by RNA/DNA interference systems in bacteria.


Teaching activities

Since 2009 –  professor at the Department of Molecular Biology, Biological Faculty, M.V. Lomonosov Moscow State University.
Since 2009 – teaching at the Scientific and Educational Center of the Institute of Molecular Genetics.
Supervisor of 3 Ph.D. studends, 5 defended PhD theses.


Awards, achievements, memberships

1) Medal of the Russian Academy of Sciences for young scientists (2009)
2) Prize of Academia Europeae for young scientists (2007)
3) Stipend of the Russian Science Support Foundation (2006-2007)
4) Stipend of the “Future of Molecular Genetics” Foundation (2003, 2005)
5) Member of the Russian Biochemical Society (2003)
6) Member of the Biochemical Society (United Kingdom) (2010)
7) Member of the American Society for Biochemistry and Molecular Biology (USA) (2012)


Publications

  1. Miropolskaya N., Feklistov A., Nikiforov V., Kulbachinskiy A. 2018. Site-specific aptamer inhibitors of Thermus RNA polymerase. Biochem. Biophys. Res. Commun. 495: 110-115.
  2. 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. Biochem J. 474: 4053–4064.
  3. Miropolskaya N., Petushkov I., Kulbachinskiy A., Makarova A.V. 2017. Identification of amino acid residues involved in the dRP-lyase activity of human Pol ι. Sci Rep. 7: 10194.
  4. Petushkov I., Esyunina D, Kulbachinskiy A. 2017. Possible roles of σ-dependent RNA polymerase pausing in transcription regulation. RNA Biol. 14: 1678-1682.
  5. Miropolskaya N., Esyunina D., Kulbachinskiy A. 2017. Conserved functions of the trigger loop and Gre factors in RNA cleavage by bacterial RNA polymerases. J. Biol. Chem. 292: 6744-6752.
  6. Agapov A, Olina A, Esyunina D, Kulbachinskiy A. 2017. Gfh factors and NusA cooperate to stimulate transcriptional pausing and termination. FEBS Lett. 591: 946-953.
  7. Petushkov I., Esyunina D., Kulbachinskiy A. 2017. s38-dependent promoter-proximal pausing by bacterial RNA polymerase. Nucleic Acids Res. 45: 3006-3016.
  8. Agapov A, Esyunina D, Pupov D, Kulbachinskiy A. 2016. Regulation of transcription initiation by Gfh factors from Deinococcus radiodurans. Biochemical Journal 473: 4493-4505.
  9. Esyunina D., Agapov A., Kulbachinskiy A. 2016. Regulation of transcriptional pausing through the secondary channel of RNA polymerase. Proc. Natl. Acad. Sci. USA. 113: 8699-8704.
  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 Res. 44: 1298-1308.
  11. Miropolskaya N., Kulbachinskiy A. 2016. Aptamers to the sigma factor mimic promoter recognition and inhibit transcription initiation by bacterial RNA polymerase. Biochem Biophys Res Commun. 469: 294-299.
  12. Esyunina D.M., Kulbachinskiy A.V. 2015. Purification and charactrerization of recombinant deinococcus radiodurans RNA polymerase. Biochemistry (Moscow) 80: 1271-1278.
  13. Agapov A., Kulbachinskiy A. Mechanisms of Stress Resistance and Gene regulation in the Radioresistant Bacterium Deinococcus radiodurans. Biochemistry (Moscow) 80: 1201-1216.
  14. Petushkov I., Pupov D., Bass I., Kulbachinskiy A. 2015. Mutations in the CRE pocket of bacterial RNA polymerase affect multiple steps of transcription. Nucleic Acids Res. 43:5798-5809.
  15. Pupov D., Kulbachinskiy A. 2015. Single-stranded DNA aptamers for functional probing of bacterial RNA polymerase. Methods Mol. Biol. 1276:165-183.
  16. Esyunina D., Klimuk E., Severinov K., Kulbachinskiy A. 2015. Distinct pathways of RNA polymerase regulation by a phage-encoded factor. Proc. Natl. Acad. Sci. USA. 112: 2017-2022.
  17. Makarova A.V., Ignatov A., Miropolskaya N., Kulbachinskiy A. 2014. Roles of the active site residues and metal cofactors in noncanonical base-pairing during catalysis by human DNA polymerase iota. DNA Repair (Amst). 22: 67-76.
  18. Basu R.S., Warner B.A., Molodtsov V., Pupov D., Esyunina D., Fernández-Tornero C., Kulbachinskiy A., Murakami K.S. 2014. Structural basis of transcription initiation by bacterial RNA polymerase holoenzyme. J. Biol. Chem. 89: 24549-24559.
  19. Tagami S., Sekine S., Minakhin L., Esyunina D., Akasaka R., Shirouzu M., Kulbachinskiy A., Severinov K., Yokoyama S. 2014. Structural basis for promoter specificity switching of RNA polymerase by a phage factor. Genes Dev. 28: 521-531.
  20. Pupov D., Kuzin I., Bass I., Kulbachinskiy A. 2014. Distinct functions of the RNA polymerase s subunit region 3.2 in RNA priming and promoter escape. Nucl. Acids Res., 42: 4494-4504.
  21. Miropolskaya N., Esyunina D., Klimašauskas S., Nikiforov V., Artsimovitch I., Kulbachinskiy A. 2014. Interplay between the trigger loop and the F loop during RNA polymerase catalysis. Nucl. Acids Res. 42: 544-552.
  22. Pupov D., Esyunina D., Feklistov A., Kulbachinskiy A. 2013. Single-strand promoter traps for bacterial RNA polymerase. Biochemical Journal. 452(2):241-248.
  23. 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 s subunits from Escherichia coli and Thermus aquaticus in transcription initiation. J. Biol. Chem. 287(28): 23779-23789.
  24. Makarova A.V., Kulbachinskiy A.V. 2012. Structure of human DNA polymerase iota and the mechanism of DNA synthesis. Biochemistry (Mosc.) 77: 547-561.
  25. Berdygulova Zh., Esyunina D., Miropolskaya N., Mukhamedyarov D., Kuznedelov K., Nickels B.E., Severinov K., Kulbachinskiy A., Minakhin L. 2012. A novel phage-encoded transcription antiterminator acts by suppressing pausing by bacterial RNA polymerase. Nucleic Acids Res. 40(9): 4052-4063.
  26. Zhilina E., Esyunina D., Brodolin K., Kulbachinskiy A. 2012. Structural transitions in the transcription elongation complexes of bacterial RNA polymerase during s-dependent pausing. Nucl. Acids Res. 40: 3078-3091.
  27. Zhilina E.V., Miropolskaya N.A., Bass I.A., Brodolin K.L., Kulbachinskiy A.V. 2011. Characteristics of σ-dependent pausing by RNA polymerases from Escherichia coli and Thermus aquaticus. Biochemistry (Mosc). 76: 1098-1106.
  28. Miropolskaya N., Nikiforov V., Klimasauskas S., Artsimovitch I.,  Kulbachinskiy A. 2010. Modulation of RNA polymerase activity through trigger loop folding. Transcription 1: 89 – 94.
  29. Pupov D., Miropolskaya N., Sevostyanova A., Bass I., Artsimovitch I., Kulbachinskiy A. 2010. Multiple roles of the RNA polymerase b¢ SW2 region in transcription initiation, promoter escape, and RNA elongation. Nucl. Acids Res. 38: 5784-5796.
  30. Pupov D.V., Kul'bachinskiĭ A.V. 2010. Structural dynamics of the active center of multisubunit RNA polymerases during RNA synthesis and proofreading. Mol Biol (Mosk). 44: 573-590.
  31. Miropolskaya N., Artsimovitch I., Klimasauskas S., Nikiforov V., Kulbachinskiy A. 2009. Allosteric control of catalysis by the F-loop of RNA polymerase. Proc. Natl. Acad. Sci. USA. 106: 18942-18947.
  32. Barinova N., Kuznedelov K., Severinov K., Kulbachinskiy A. 2008. Structural modules of RNA polymerase required for transcription from promoters containing downstream basal promoter element GGGA. J. Biol. Chem. 283: 22482-22489.
  33. Pupov D.V., Barinova N.A., Kulbachinskiy A.V. 2008. Analysis of RNA Cleavage by RNA Polymerases from Escherichia coli and Deinococcus radiodurans. Biochemistry (Mosc). 2008 73: 725-729.
  34. Barinova N., Zhilina E., Bass I., Nikiforov V., Kulbachinskiy A. 2008. Lineage-specific amino acid substitutions in region 2 of the RNA polymerase s subunit affect the temperature of promoter opening. J. Bacteriol. 190: 3088-3092.
  35. Kulbachinskiy A.V. Methods for selection of aptamers to protein targets. 2007. Biochemistry (Moscow) 72: 1505-1518.
  36. Sevostyanova A, Feklistov A, Barinova N, Heyduk E, Bass I, Klimasauskas S, Heyduk T, Kulbachinskiy A. 2007. Specific recognition of the -10 promoter element by the free RNA polymerase sigma subunit. J. Biol. Chem. 282: 22033-22039.
  37. Zenkin N., Kulbachinskiy A., Yuzenkova Y., Mustaev A., Bass I., Severinov K., Brodolin K. 2007. Region 1.2 of the RNA polymerase sigma subunit controls recognition of the -10 promoter element. EMBO J. 26: 955-964.
  38. Feklistov A., Barinova N., Sevostyanova A., Heyduk E., Bass I., Vvedenskaya I., Kuznedelov K., Merkienė E., Stavrovskaya E., Klimašauskas S., Nikiforov V., Heyduk T., Severinov K., Kulbachinskiy A. 2006. A basal promoter element recognized by free RNA polymerase sigma subunit determines promoter recognition by RNA polymerase holoenzyme. Mol. Cell. 23: 97-107.
  39. Kulbachinskiy A., Mustaev A. 2006. Region 3.2 of the sigma subunit contributes to the binding of the 3'-initiating nucleotide in the RNA polymerase active center and facilitates promoter clearance during initiation. J. Biol. Chem. 281: 18273-18276.
  40. Kulbachinskiy A.V., Nikiforov V.G., Brodolin K.L. 2005. Differences in the contacts of RNA polymerases from E. coli and T. aquaticus with lacUV5 promoter are determined by the core enzyme of RNA polymerase. Biochemistry (Moscow), 70: 1493 – 1497.
  41. Zenkin N., Kulbachinskiy A., Bass I., Nikiforov V. 2005. 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. 49: 1587-1590.
  42. Kulbachinskiy A., Feklistov A., Krasheninnikov I., Goldfarb A., Nikiforov V. 2004. Aptamers to E. coli core RNA polymerase that sense its interaction with rifampicin, s subunit and GreB. Eur. J. Biochem., 271: 4921-4931.
  43. Kulbachinskiy A., Bass I., Bogdanova E., Goldfarb A., Nikiforov V. 2004. Cold sensitivity of thermophilic and mesophilic RNA polymerases. J. Bacteriol., 186: 7818-7820.
  44. Kul'bachinskiĭ A.V., Ershova G.V., Korzheva N.V., Brodolin K.L., Nikiforov V.G. 2002. Mutations in β’-subunit of the Escherichia coli RNA polymerase influence interaction with the downstream DNA duplex in the elongation complex. Genetika (Russian), 38: 1207-1211.
  45. Kulbachinskiy A., Mustaev A., Goldfarb A., Nikiforov V. 1999. Interaction with free beta' subunit unmasks DNA-binding domain of RNA polymerase sigma subunit. FEBS Lett., 454: 71-74.