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Transcription inactivation through local refolding of the RNA polymerase structure

Abstract

Structural studies of antibiotics not only provide a shortcut to medicine allowing for rational structure-based drug design, but may also capture snapshots of dynamic intermediates that become ‘frozen’ after inhibitor binding1,2. Myxopyronin inhibits bacterial RNA polymerase (RNAP) by an unknown mechanism3. Here we report the structure of dMyx—a desmethyl derivative of myxopyronin B4—complexed with a Thermus thermophilus RNAP holoenzyme. The antibiotic binds to a pocket deep inside the RNAP clamp head domain, which interacts with the DNA template in the transcription bubble5,6. Notably, binding of dMyx stabilizes refolding of the β′-subunit switch-2 segment, resulting in a configuration that might indirectly compromise binding to, or directly clash with, the melted template DNA strand. Consistently, footprinting data show that the antibiotic binding does not prevent nucleation of the promoter DNA melting but instead blocks its propagation towards the active site. Myxopyronins are thus, to our knowledge, a first structurally characterized class of antibiotics that target formation of the pre-catalytic transcription initiation complex—the decisive step in gene expression control. Notably, mutations designed in switch-2 mimic the dMyx effects on promoter complexes in the absence of antibiotic. Overall, our results indicate a plausible mechanism of the dMyx action and a stepwise pathway of open complex formation in which core enzyme mediates the final stage of DNA melting near the transcription start site, and that switch-2 might act as a molecular checkpoint for DNA loading in response to regulatory signals or antibiotics. The universally conserved switch-2 may have the same role in all multisubunit RNAPs.

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Figure 1: Structure of the RNAP–Myx complex.
Figure 2: Effect of RNAP mutations on dMyx activity.
Figure 3: A mechanism of the dMyx action.
Figure 4: Mutations in switch-2 affect the open complex formation.

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Protein Data Bank

Data deposits

The atomic coordinates and structure factors have been in deposited in the PDB under accession number 3EQL.

References

  1. Brueckner, F. & Cramer, P. Structural basis of transcription inhibition by α-amanitin and implications for RNA polymerase II translocation. Nature Struct. Mol. Biol. 15, 811–818 (2008)

    CAS  Article  Google Scholar 

  2. Vassylyev, D. G. et al. Structural basis for substrate loading in bacterial RNA polymerase. Nature 448, 163–168 (2007)

    ADS  CAS  Article  Google Scholar 

  3. Irschik, H., Gerth, K., Hofle, G., Kohl, W. & Reichenbach, H. The myxopyronins, new inhibitors of bacterial RNA synthesis from Myxococcus fulvus (Myxobacterales). J. Antibiot. (Tokyo) 36, 1651–1658 (1983)

    CAS  Article  Google Scholar 

  4. Lira, R. et al. Syntheses of novel myxopyronin B analogs as potential inhibitors of bacterial RNA polymerase. Bioorg. Med. Chem. Lett. 17, 6797–6800 (2007)

    CAS  Article  Google Scholar 

  5. Paget, M. S. & Helmann, J. D. The σ70 family of sigma factors. Genome Biol. 4, 203 (2003)

    Article  Google Scholar 

  6. Artsimovitch, I., Kahmeyer-Gabbe, M. & Howe, M. M. Distortion in the spacer region of Pm during activation of middle transcription of phage Mu. Proc. Natl Acad. Sci. USA 93, 9408–9413 (1996)

    ADS  CAS  Article  Google Scholar 

  7. Chen, Y. F. & Helmann, J. D. DNA-melting at the Bacillus subtilis flagellin promoter nucleates near -10 and expands unidirectionally. J. Mol. Biol. 267, 47–59 (1997)

    CAS  Article  Google Scholar 

  8. Li, X. Y. & McClure, W. R. Stimulation of open complex formation by nicks and apurinic sites suggests a role for nucleation of DNA melting in Escherichia coli promoter function. J. Biol. Chem. 273, 23558–23566 (1998)

    CAS  Article  Google Scholar 

  9. Kettenberger, H., Armache, K. J. & Cramer, P. Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol. Cell 16, 955–965 (2004)

    CAS  Article  Google Scholar 

  10. Vassylyev, D. G., Vassylyeva, M. N., Perederina, A., Tahirov, T. H. & Artsimovitch, I. Structural basis for transcription elongation by bacterial RNA polymerase. Nature 448, 157–162 (2007)

    ADS  CAS  Article  Google Scholar 

  11. Murakami, K. S., Masuda, S., Campbell, E. A., Muzzin, O. & Darst, S. A. Structural basis of transcription initiation: an RNA polymerase holoenzyme–DNA complex. Science 296, 1285–1290 (2002)

    ADS  CAS  Article  Google Scholar 

  12. Craig, M. L. et al. DNA footprints of the two kinetically significant intermediates in formation of an RNA polymerase-promoter open complex: evidence that interactions with start site and downstream DNA induce sequential conformational changes in polymerase and DNA. J. Mol. Biol. 283, 741–756 (1998)

    CAS  Article  Google Scholar 

  13. Davis, C. A., Bingman, C. A., Landick, R., Record, M. T. & Saecker, R. M. Real-time footprinting of DNA in the first kinetically significant intermediate in open complex formation by Escherichia coli RNA polymerase. Proc. Natl Acad. Sci. USA 104, 7833–7838 (2007)

    ADS  CAS  Article  Google Scholar 

  14. Suh, W.-C., Ross, W. & Record, M. T. Two open complexes and a requirement for Mg2+ to open the λ PR transcription start site. Science 259, 358–361 (1993)

    ADS  CAS  Article  Google Scholar 

  15. Severinov, K. & Darst, S. A. A mutant RNA polymerase that forms unusual open promoter complexes. Proc. Natl Acad. Sci. USA 94, 13481–13486 (1997)

    ADS  CAS  Article  Google Scholar 

  16. Cramer, P., Bushnell, D. A. & Kornberg, R. D. Structural basis of transcription: RNA polymerase II at 2.8 ångstrom resolution. Science 292, 1863–1876 (2001)

    ADS  CAS  Article  Google Scholar 

  17. Gnatt, A. L., Cramer, P., Fu, J., Bushnell, D. A. & Kornberg, R. D. Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 Å resolution. Science 292, 1876–1882 (2001)

    ADS  CAS  Article  Google Scholar 

  18. Belogurov, G. A. et al. Structural basis for converting a general transcription factor into an operon-specific virulence regulator. Mol. Cell 26, 117–129 (2007)

    CAS  Article  Google Scholar 

  19. Kuznedelov, K., Korzheva, N., Mustaev, A. & Severinov, K. Structure-based analysis of RNA polymerase function: the largest subunit’s rudder contributes critically to elongation complex stability and is not involved in the maintenance of RNA–DNA hybrid length. EMBO J. 21, 1369–1378 (2002)

    CAS  Article  Google Scholar 

  20. Vassylyeva, M. N. et al. Purification, crystallization and initial crystallographic analysis of RNA polymerase holoenzyme from Thermus thermophilus . Acta Crystallogr. D 58, 1497–1500 (2002)

    Article  Google Scholar 

  21. Artsimovitch, I. et al. Structural basis for transcription regulation by alarmone ppGpp. Cell 117, 299–310 (2004)

    CAS  Article  Google Scholar 

  22. Vassylyev, D. G. et al. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution. Nature 417, 712–719 (2002)

    ADS  CAS  Article  Google Scholar 

  23. Artsimovitch, I. et al. Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins. Cell 122, 351–363 (2005)

    CAS  Article  Google Scholar 

  24. Temiakov, D. et al. Structural basis of transcription inhibition by antibiotic streptolydigin. Mol. Cell 19, 655–666 (2005)

    CAS  Article  Google Scholar 

  25. Vassylyev, D. G. et al. Structural basis for transcription inhibition by tagetitoxin. Nature Struct. Mol. Biol. 12, 1086–1093 (2005)

    CAS  Article  Google Scholar 

  26. Otwinowski, Z. & Minor, W. Processing X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997)

    CAS  Article  Google Scholar 

  27. Brunger, A. T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998)

    CAS  Article  Google Scholar 

  28. Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991)

    Article  Google Scholar 

  29. Kraulis, P. J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946–950 (1991)

    Article  Google Scholar 

  30. Esnouf, R. M. Further additions to MolScript version 1.4, including reading and contouring of electron-density maps. Acta Crystallogr. D 55, 938–940 (1999)

    CAS  Article  Google Scholar 

  31. Merritt, E. A. & Bacon, D. J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505–524 (1997)

    CAS  Article  Google Scholar 

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Acknowledgements

We thank T. Townes for critical reading of the manuscript and R. Saecker for many stimulating discussions. Use of the Advanced Photon Source was supported by the US Department of Energy, Office of Energy Research under contract No. W-31-109-Eng-38. This work was supported by National Institutes of Health grants to I.A. and D.G.V.

Author Contributions J.R.A., A.X.X., R.L. and S.E.W. synthesized the antibiotic. G.A.B. constructed, purified and analysed the properties of mutationally altered RNAPs. M.N.V. performed crystallization. M.N.V. and S.K. carried out data collection and processing. A.S. performed footprinting analysis. I.A. carried out vector construction, performed biochemical assays, and supervised functional analysis of the dMyx mechanism. E.N. contributed to data analysis. D.G.V. has determined, refined, analysed the structure and supervised the project. D.G.V. and I.A. jointly wrote the manuscript.

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Correspondence to Irina Artsimovitch or Dmitry G. Vassylyev.

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Belogurov, G., Vassylyeva, M., Sevostyanova, A. et al. Transcription inactivation through local refolding of the RNA polymerase structure. Nature 457, 332–335 (2009). https://doi.org/10.1038/nature07510

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