Cell Biology

Faculty and Research Interests

Sergei Borukhov, PhD

(Updated January 2017)

  1. Lee J, Borukhov S. Bacterial RNA Polymerase-DNA Interaction-The Driving Force of Gene Expression and the Target for Drug Action. Front Mol Biosci, 3(73); 1 – 15, November 2016.
  2. Lerner E, Chung S, Allen BL, Wang S, Lee J, Lu SW, Grimaud LW, Ingargiola A, Michalet X, Alhadid Y, Borukhov S, Strick TR, Taatjes DJ, Weiss S. Backtracked and paused transcription initiation intermediate of Escherichia coli RNA polymerase. Proc Natl Acad Sci,113(43): E6562-71, October 2016.
  3. Parshin A, Shiver AL, Lee J, Ozerova M, Schneidman-Duhovny D, Gross CA, Borukhov S. DksA regulates RNA polymerase in Escherichia coli through a network of interactions in the secondary channel that includes Sequence Insertion 1. Proc Natl Acad Sci, 112(50): E6862-71, December 2015.
  4. Yakunina M, Artamonova T, Borukhov S, Makarova KS, Severinov K, Minakhin L. A non-canonical multisubunit RNA polymerase encoded by a giant bacteriophage. Nucleic Acids Res, 43(21): 10411-20, December 2015.
  5. Mekler V, Minakhin L, Borukhov S, Mustaev A, Severinov K. Coupling of downstream RNA polymerase-promoter interactions with formation of catalytically competent transcription initiation complex. J Mol Biol, 426(24): 3973-84, December 2014.
  6. Kulikovsky A, Serebryakova M, Bantysh O, Metlitskaya A, Borukhov S, Severinov K, Dubiley S.The molecular mechanism of aminopropylation of peptide-nucleotide antibiotic microcin C. J Am Chem Soc, 136(31): 11168-75, August 2014.
  7. Stepanova E, Wang M, Severinov K, Borukhov S. Early transcriptional arrest at Escherichia coli rplN and ompX promoters. J Biol Chem, 18; 284(51): 35702-13, Dec 2009.
  8. Borukhov S, Nudler E. RNA polymerase: the vehicle of transcription. Trends Microbiol, 6(3):126-34, Mar 2008.
  9. Epshtein V, Cardinale CJ, Ruckenstein AE, Borukhov S, Nudler E. An allosteric path to transcription termination. Mol Cell, 28; 28(6): 991-1001, Dec 2007.
  10. Stepanova E, Lee J, Ozerova M, Semenova E, Datsenko K, Wanner BL, Severinov K, Borukhov S. Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro. J Bacteriol, 189(24): 8772-85, Dec 2007.
  11. Cava F, Laptenko O, Borukhov S, Chahlafi Z, Blas-Galindo E, Gómez-Puertas P, Berenguer J. Control of the respiratory metabolism of Thermus thermophilus by the nitrate respiration conjugative element NCE. Mol Microbiol, 64(3): 630-46, May 2007.
  12. Zlatanova J, McAllister WT, Borukhov S, Leuba SH. Single-molecule approaches reveal the idiosyncrasies of RNA polymerases. Structure, 14(6): 953-66, Jun 2006.
  13. Laptenko O, Kim SS, Lee J, Starodubtseva M, Cava F, Berenguer J, Kong XP, Borukhov S. pH-dependent conformational switch activates the inhibitor of transcription elongation. EMBO J, 25(10): 2131-41, May 2006.
  14. Tuske S, Sarafianos SG, Wang X, Hudson B, Sineva E, Mukhopadhyay J, Birktoft JJ, Leroy O, Ismail S, Clark AD Jr, Dharia C, Napoli A, Laptenko O, Lee J, Borukhov S, Ebright RH, Arnold E. Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation. Cell, 26; 122(4): 541-52, Aug 2005.
  15. Borukhov S, Lee J. RNA polymerase structure and function at lac operon. C R Biol, 328(6):576-87, June 2005, Review.
  16. Borukhov S, Lee J, Laptenko O. Bacterial transcription elongation factors: new insights into molecular mechanism of action. Mol Microbiol, 55(5):1315-24, Mar 2005, Review.
  17. Unbehaun A, Borukhov SI, Hellen CU, Pestova TV. Release of initiation factors from 48S complexes during ribosomal subunit joining and the link between establishment of codon-anticodon base-pairing and hydrolysis of eIF2-bound GTP. Genes Dev, 15; 18(24): 3078-93, Dec 2004.
  18. Adelman K, Yuzenkova J, La Porta 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, 18; 14(6): 753-62, Jun 2004.
  19. Laptenko O, Borukhov S. Biochemical assays of Gre factors of Thermus thermophilus. Methods Enzymol, 371: 219-32, 2003.
  20. Laptenko O, Lee J, Lomakin I, Borukhov S. Transcript cleavage factors GreA and GreB act as transient catalytic components of RNA polymerase. EMBO J, 1; 22(23): 6322-34, Dec 2003.
  21. Epshtein V, Toulmé F, Rahmouni AR, Borukhov S, Nudler E. Transcription through the roadblocks: the role of RNA polymerase cooperation. EMBO J, 15; 22(18): 4719-27, Sep 2003.
  22. Borukhov S, Nudler E. RNA polymerase holoenzyme: structure, function and biological implications. Curr Opin Microbiol, 6(2): 93-100, Apr 2003, Review.
  23. Role of the RNA polymerase sigma subunit in transcription initiation. Borukhov S, Severinov K. Res Microbiol, 153(9): 557-62, Nov 2002, Review.
  24. Purification, crystallization and initial crystallographic analysis of RNA polymerase holoenzyme from Thermus thermophilus. Vassylyeva MN, Lee J, Sekine SI, Laptenko O, Kuramitsu S, Shibata T, Inoue Y, Borukhov S, Vassylyev DG, Yokoyama S. Acta Crystallogr D Biol Crystallogr, 58(9): 1497-500, Sept 2002.
  25. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution. Vassylyev DG, Sekine S, Laptenko O, Lee J, Vassylyeva MN, Borukhov S, Yokoyama S. Nature, 13;417(6890):712-9, June 2002.


  1. Borukhov, S., Polyakov, A., Nikiforov, V. & Goldfarb, A. (1992) GreA protein: a transcription elongation factor from Escherichia coli, Proc. Natl. Acad. Sci. USA., 89, 8899-8902.
  2. Borukhov, S., Sagitov, V. & Goldfarb, A. (1993) Transcript cleavage factors from E. coli. Cell 72, 459-466.
  3. Fish, R.N. & Kane, C.M. (2002) Promoting elongation with transcript cleavage stimulatory factors. Biochim. Biophys. Acta. 1577, 287-307.
  4. Deighan, P. & Hochschild, A. (2006) Conformational toggle triggers a modulator of RNA polymerase activity. Trends Biochem. Sci. 8, 424-426.
  5. Nickels, B.E. & Hochschild, A. (2004) Regulation of RNA polymerase through the secondary channel. Cell 118, 281-284.
  6. Borukhov, S., Lee, J. & Laptenko, O. (2005) Bacterial transcription elongation factors: new insights into molecular mechanism of action. Mol. Microbiol. 55, 1315-1324.
  7. Nudler, E., Mustaev, A., Lukhtanov, E. & Goldfarb, A. (1997) The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase. Cell 89, 33-41. 
  8. Komissarova, N. & Kashlev, M. (1997) Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3' end of the RNA intact and extruded. Proc. Natl. Acad. Sci. USA 94, 1755-1760.
  9. Orlova, M., Newlands, J., Das, A., Goldfarb, A. & Borukhov, S. (1995) Intrinsic transcript cleavage activity of RNA polymerase. Proc. Natl. Acad. Sci. USA 92, 4596-4600.
  10. Hsu, L.M., Vo, N.V. & Chamberlin, M.J. (1995) Escherichia coli transcript cleavage factors GreA and GreB stimulate promoter escape and gene expression in vivo and in vitro. Proc. Natl. Acad. Sci. USA 92, 11588-11592.
  11. Stepanova, E, Lee, J., Ozerova, M., Semenova, E., Datsenko, K., Wanner, B., Severinov, K., and Borukhov, S. (2007) Analysis of promoter targets for E. coli transcription elongation factor GreA in vivo and in vitro. J. Bacteriol., 189, 8772-8785.
  12. Kapanidis, A.N., Margeat, E., Ho, S.O., Kortkhonjia, E., Weiss, S. & Ebright, R.H. (2006) Initial transcription by RNA polymerase proceeds through a DNA scrunching mechanism. Science (in press).
  13. Hsu, L.M. (2002) Promoter clearance and escape in prokaryotes. Biochim. Biophys. Acta 1577, 191-207.
  14. Trautinger, B.W., Jaktaji, R.P., Rusakova, E. & Lloyd, R.G. (2005) RNA polymerase modulators and DNA repair activities resolve conflicts between DNA replication and transcription. Mol Cell. 19, 247-258. 
  15. Mirkin, E.V., Castro, R.D., Nudler, E., & Mirkin, S.M. (2006) Transcription regulatory elements are punctuation marks for DNA replication. Proc Natl Acad Sci U S A. 103, 7276-7281.
  16. Rutherford S.T, Lemke J.J., Vrentas C.E, Gaal T., Ross W., Gourse R.L.(2007) Effects of DksA, GreA, and GreB on transcription initiation: insights into the mechanisms of factors that bind in the secondary channel of RNA polymerase. J Mol Biol. 366, 1243-1257.
  17. Stebbins, C.E., Borukhov, S., Orlova, M., Polyakov, A., Goldfarb, A. & Darst, S.A. (1995) Crystal structure of the GreA transcript cleavage factor from Escherichia coli. Nature 373, 636-640.
  18. Koulich, D., Orlova, M., Malhotra, A., Sali, A., Darst, S.A. & Borukhov, S. (1997) Domain organization of Escherichia coli transcript cleavage factors GreA and GreB. J. Biol. Chem. 272, 7201-7210.
  19. Vassylyeva, M.N., Svetlov, V., Dearborn, A.D,, Klyuyev, S., Artsimovitch, I., Vassylyev D.G (2007) The carboxy-terminal coiled-coil of the RNA polymerase beta'-subunit is the main binding site for Gre factors. EMBO Rep. 8, 1038-1043.
  20. Koulich, D., Nikiforov, V. & Borukhov, S. (1998) Distinct functions of N and C-terminal domains of GreA, an Escherichia coli transcript cleavage factor. J. Mol. Biol. 276, 379-389.
  21. Kulish, D., Lee, J., Lomakin, I., Nowicka, B., Das, A., Darst, S., Normet, K. & Borukhov, S. (2000) The functional role of basic patch, a structural element of Escherichia coli transcript cleavage factors GreA and GreB. J. Biol. Chem. 275, 12789-12798.
  22. Laptenko, O., Lee, J., Lomakin, I. & Borukhov, S. (2003) Transcript cleavage factors GreA and GreB act as transient catalytic components of RNA polymerase. EMBO J. 22, 6322-6334.
  23. Polyakov, A., Richter, C., Malhotra, A., Koulich, D., Borukhov, S., & Darst, S.A. (1998) Visualization of the binding site for the transcript cleavage factor GreB on Escherichia coli RNA polymerase. J. Mol. Biol. 281, 465-473.
  24. Kettenberger, H., Armache, K.J., & Cramer, P. (2003) Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage. Cell 114, 347-357.
  25. Laptenko, O., Hartsch, T., Bozhkov, A.I. & Borukhov, S. (2000) Gre-homologous transcription factors GreA-1 and GreA-2 from Thermus thermophilus: cloning, purification and analysis of functional activity. Biologicheskiy Vestnik (Biological Herald of Ukrainian Academy of Sciences) 4, 3-14.
  26. Laptenko, O. & Borukhov, S. (2003) Biochemical assays of Gre factors of Thermus thermophilus. Methods Enzymol. 371, 219-232.
  27. Symersky, J., Perederina, A., Vassylyeva, M.N., Svetlov, V., Artsimovitch, I. & Vassylyev, D.G. (2006) Regulation through the RNA polymerase secondary channel: Structural and functional variability of the coiled-coil transcription factors. J. Biol. Chem. 281, 1309-1312.
  28. Laptenko, O., Kim, S.S., Lee, J., Starodubtseva, M., Cava, F., Berenguer, J., Kong, X.P. & Borukhov, S. (2006) pH-dependent conformational switch activates the inhibitor of transcription elongation. EMBO J. 25, 2131-2141.
  29. Paul, B.J., Ross, W., Gaal, T., & Gourse, R.L. (2004) rRNA transcription in Escherichia coli. Annu Rev Genet. 38, 749-770.
  30. Perederina, A., Svetlov, V., Vassylyeva, M.N., Tahirov, T.H., Yokoyama, S., Artsimovitch, I., and Vassylyev, D.G. (2004) Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription. Cell 118, 297-309.
  31. Potrykus, K., Vinella, D., Murphy, H., Szalewska-Palasz, A., D’Ari, R. & Cashel, M. (2006) Antagonistic regulation of Escherichia coli ribosomal RNA rrnB P1 promoter activity by GreA and DksA. J. Biol. Chem. 281, 15238-15248.

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