Laboratory of Molecular Genetics of Microorganisms | Institute of Molecular Genetics

Kulbachinskiy Andrey Vladimirovich


List of staff

Alexey Agapov, Ph.D. student
Daria Esyunina, Research Scientist, Ph.D.
Artem Ignatov, Ph.D. student
Natalia Khachikian, technician
Andrey Kulbachinskiy, lab head, D.Sci.
Anton Kurakov, Ph.D. student
Tamara Logutenkova, technician
Nataliya Miropolskaya, Senior Research Scientist, Ph.D.
Sofia Mindlin, Leading Research Scientist, D.Sci.
Vadim Nikiforov, Leading Research Scientist, D.Sci. 
Maya Petrova, head of the Sector of storage and analysis of microorganisms, D.Sci.
Ivan Petushkov, Ph.D. student
Danil Pupov, Senior Research Scientist, Ph.D.

Press the picture for enlarge

(from left to right)
D. Pupov, N. Miropolskaya, A. Agapov, A. Kulbachinskiy, A. Kurakov, I. Petushkov, T. Logutenkova (2nd raw),
N Khachikian, D. Esyunina, M. Petrova, S. Mindlin (1st raw)


Main directions of research

- Analysis of the mechanisms of transcription initiation by RNA polymerases containing major and alternative sigma factors
- Analysis of the mechanisms of catalysis in the active site of bacterial RNA polymerase
- Comparison of RNA polymerases from various bacteria, including extremophiles
- Development of aptamers to RNA polymerase and transcription factors
- Studies of the mechanisms of transcription and replication of damaged DNA
- Analysis of the interplay between transcription, DNA repair and replication

The laboratory was organized in 1959 by an outstanding Russian scientist, one of the founders of the Molecular Genetics discipline, Roman B. Khesin. From 1985 to 2004 the laboratory was headed by Vadim G. Nikiforov. From 2005 the head of laboratory is Andrey Kulbachinskiy. In 2009, the Sector of storage and analysis of microorganisms, headed by Maya Petrova, was established within the laboratory.



  1. 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.
  2. 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.
  3. Petushkov I., Esyunina D., Kulbachinskiy A. 2017. s38-dependent promoter-proximal pausing by bacterial RNA polymerase. Nucleic Acids Res. 45: 3006-3016.
  4. Agapov A, Esyunina D, Pupov D, Kulbachinskiy A. 2016. Regulation of transcription initiation by Gfh factors from Deinococcus radiodurans. Biochemical Journal 473: 4493-4505.
  5. 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.
  6. 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.
  7. 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.
  8. Esyunina D.M., Kulbachinskiy A.V. 2015. Purification and charactrerization of recombinant deinococcus radiodurans RNA polymerase. Biochemistry (Moscow) 80: 1271-1278.
  9. Agapov A., Kulbachinskiy A. Mechanisms of Stress Resistance and Gene regulation in the Radioresistant Bacterium Deinococcus radiodurans. Biochemistry (Moscow) 80: 1201-1216.
  10. 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.
  11. Pupov D., Kulbachinskiy A. 2015. Single-stranded DNA aptamers for functional probing of bacterial RNA polymerase. Methods Mol. Biol. 1276:165-183.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. Pupov D., Esyunina D., Feklistov A., Kulbachinskiy A. 2013. Single-strand promoter traps for bacterial RNA polymerase. Biochemical Journal. 452(2):241-248.
  19. 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.
  20. Makarova A.V., Kulbachinskiy A.V. 2012. Structure of human DNA polymerase iota and the mechanism of DNA synthesis. Biochemistry (Mosc.) 77: 547-561.
  21. 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.
  22. 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.
  23. 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.
  24. Miropolskaya N., Nikiforov V., Klimasauskas S., Artsimovitch I.,  Kulbachinskiy A. 2010. Modulation of RNA polymerase activity through trigger loop folding. Transcription 1: 89 – 94.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. 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.
  31. Kulbachinskiy A.V. Methods for selection of aptamers to protein targets. 2007. Biochemistry (Moscow) 72: 1505-1518.
  32. 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.
  33. 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.
  34. 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.
  35. 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.
  36. 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.
  37. 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.
  38. 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.
  39. Kulbachinskiy A., Bass I., Bogdanova E., Goldfarb A., Nikiforov V. 2004. Cold sensitivity of thermophilic and mesophilic RNA polymerases. J. Bacteriol., 186: 7818-7820.
  40. 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.
  41. 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.
  42. Kashlev M, Lee J, Zalenskaya K, Nikiforov V, Goldfarb A. 1990. Blocking of the initiation-to-elongation transition by a transdominant RNA polymerase mutation. Science. 248:1006-1009.
  43. Ovchinnikov Y.A., Monastyrskaya G.S., Guriev S.O., Kalinina N.F., Sverdlov E.D., Gragerov A.I., Bass I.A., Kiver I.F., Moiseyeva E.P., Igumnov V.N., Mindlin S.Z., Nikiforov V.G., Khesin RB. 1983. RNA polymerase rifampicin resistance mutations in Escherichia coli: sequence changes and dominance. Mol. Gen. Genet. 190: 344-348.
  44. Ovchinnikov YuA, Monastyrskaya GS, Gubanov VV, Lipkin VM, Sverdlov ED, Kiver IF, Bass IA, Mindlin SZ, Danilevskaya ON, Khesin RB. Primary structure of Escherichia coli RNA polymerase nucleotide substitution in the beta subunit gene of the rifampicin resistant rpoB255 mutant. Mol Gen Genet. 1981;184(3):536-8.
  45. Gragerov AI, Kocherginskaya SA, Larionov OA, Kalyaeva ES, Nikiforov VG. Cold-sensitive mutations in beta and beta' subunit gene affecting the interaction of RNA polymerase with promoters. Mol Gen Genet. 1980;180(2):399-403.
  46. Dmitriev AD, Danilevskaya ON, Khesin RB. The influence of mutations upon the synthesis of RNA polymerase subunits in Escherichia coli cells. Mol Gen Genet. 1976 Jun 15;145(3):317-26.
  47. Nikiforov VG. Substrate dependent heterogeneity of initiation by RNA polymerase from thermophilic B. megaterium. FEBS Lett. 1970 Sep 6;9(3):186-188.
  48. Khesin RB, Shemyakin MF, Gorlenko AM, Mindlin SZ, Ilyina TS. Studies on the RNA polymerase in Escherichia coli K12 using the mutation affecting its activity. J Mol Biol. 1969 Jun 28;42(3):401-11.
  49. Khesin RB, Gorlenko ZM, Shemyakin MF, Stvolinsky SL, Mindlin SZ, Ilyina TS. Studies on the functions of the RNA polymerase components by means of mutations. Mol Gen Genet. 1969;105(3):243-61.
  50. Khesin RB, Mindlin SZ, Gorlenko ZM, Ilyina TS. Temperature sensitive mutations affecting RNA synthesis in Escherichia coli. Mol Gen Genet. 1968;103(2):194-208.
  51. Bass IA, Kamzolova SG, Shemiakin MF, Gorlenko ZhM, Astaurova OB, Khesin RB. On the specificity of RNA synthesis during phage infection. Biokhimiia. 1966 Sep-Oct;31(5):910-7.
  52. KHESIN RB, SHEMIAKIN MF. [Some properties of messenger ribonucleic acids and their complexes with desoxyribonucleic acids] Biokhimiia. 1962 Sep-Oct;27:761-79.
  53. KHESIN RB, SHEMIAKIN MF, GORLENKO ZhM, BOGDANOVA SL, AFANAS'EVA TP. RNA polymerase in E. coli cells infected with T2 phage Biokhimiia. 1962 Nov-Dec;27:1092-1105.