Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

An allosteric mechanism of Rho-dependent transcription termination

Nature volume 463, pages 245–249 (2010)Cite this article

Subjects

A Corrigendum to this article was published on 19 August 2010

Abstract

Rho is the essential RNA helicase that sets the borders between transcription units and adjusts transcriptional yield to translational needs in bacteria1,2,3. Although Rho was the first termination factor to be discovered4, the actual mechanism by which it reaches and disrupts the elongation complex (EC) is unknown. Here we show that the termination-committed Rho molecule associates with RNA polymerase (RNAP) throughout the transcription cycle; that is, it does not require the nascent transcript for initial binding. Moreover, the formation of the RNAP–Rho complex is crucial for termination. We show further that Rho-dependent termination is a two-step process that involves rapid EC inactivation (trap) and a relatively slow dissociation. Inactivation is the critical rate-limiting step that establishes the position of the termination site. The trap mechanism depends on the allosterically induced rearrangement of the RNAP catalytic centre by means of the evolutionarily conserved mobile trigger-loop domain, which is also required for EC dissociation. The key structural and functional similarities, which we found between Rho-dependent and intrinsic (Rho-independent) termination pathways, argue that the allosteric mechanism of termination is general and likely to be preserved for all cellular RNAPs throughout evolution.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Uncoupling EC inactivation from dissociation at Rho termination sites.
Figure 2: EC inactivation (trap) by Rho is accompanied by a rearrangement of protein–RNA contacts in the catalytic centre.
Figure 3: Effect of RNAP mutations, heterologous (T7) RNAP and tagetitoxin (Tgt) on Rho termination.
Figure 4: Functional Rho binds RNAP throughout the transcription cycle.

Similar content being viewed by others

References

  1. Adhya, S. & Gottesman, M. Control of transcription termination. Annu. Rev. Biochem. 47, 967–996 (1978)

    Article  CAS  Google Scholar 

  2. Richardson, J. P. Preventing the synthesis of unused transcripts by Rho factor. Cell 64, 1047–1049 (1991)

    Article  CAS  Google Scholar 

  3. Cardinale, C. J. et al. Termination factor Rho and its cofactors NusA and NusG silence foreign DNA in E. coli . Science 320, 935–938 (2008)

    Article  ADS  CAS  Google Scholar 

  4. Roberts, J. W. Termination factor for RNA synthesis. Nature 224, 1168–1174 (1969)

    Article  ADS  CAS  Google Scholar 

  5. Geiselmann, J., Yager, T. D., Gill, S. C., Calmettes, P. & von Hippel, P. H. Physical properties of the Escherichia coli transcription termination factor Rho. 1. Association states and geometry of the Rho hexamer. Biochemistry 31, 111–121 (1992)

    Article  CAS  Google Scholar 

  6. Browne, R. J., Barr, E. W. & Stitt, B. L. Catalytic cooperativity among subunits of Escherichia coli transcription termination factor Rho. Kinetics and substrate structural requirements. J. Biol. Chem. 280, 13292–13299 (2005)

    Article  CAS  Google Scholar 

  7. Skordalakes, E. & Berger, J. M. Structural insights into RNA-dependent ring closure and ATPase activation by the Rho termination factor. Cell 127, 553–564 (2006)

    Article  CAS  Google Scholar 

  8. Adelman, J. L. et al. Mechanochemistry of transcription termination factor Rho. Mol. Cell 22, 611–621 (2006)

    Article  CAS  Google Scholar 

  9. Banerjee, S., Chalissery, J., Bandey, I. & Sen, R. Rho-dependent transcription termination: more questions than answers. J. Microbiol. 44, 11–22 (2006)

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Platt, T. Rho and RNA: models for recognition and response. Mol. Microbiol. 11, 983–990 (1994)

    Article  CAS  Google Scholar 

  11. Kim, D. E. & Patel, S. S. The kinetic pathway of RNA binding to the Escherichia coli transcription termination factor Rho. J. Biol. Chem. 276, 13902–13910 (2001)

    Article  CAS  Google Scholar 

  12. Roberts, J. W., Shankar, S. & Filter, J. J. RNA polymerase elongation factors. Annu. Rev. Microbiol. 62, 211–233 (2008)

    Article  CAS  Google Scholar 

  13. Jin, D. J., Burgess, R. R., Richardson, J. P. & Gross, C. A. Termination efficiency at Rho-dependent terminators depends on kinetic coupling between RNA polymerase and Rho. Proc. Natl Acad. Sci. USA 89, 1453–1457 (1992)

    Article  ADS  CAS  Google Scholar 

  14. Zhu, A. Q. & von Hippel, P. H. Rho-dependent termination within the trp t′ terminator. II. Effects of kinetic competition and rho processivity. Biochemistry 37, 11215–11222 (1998)

    Article  CAS  Google Scholar 

  15. Guerin, M., Robichon, N., Geiselmann, J. & Rahmouni, A. R. A simple polypyrimidine repeat acts as an artificial rho-dependent terminator in vivo and in vitro . Nucleic Acids Res. 26, 4895–4900 (1998)

    Article  CAS  Google Scholar 

  16. Chalissery, J., Banerjee, S., Bandey, I. & Sen, R. Transcription termination defective mutants of Rho: role of different functions of Rho in releasing RNA from the elongation complex. J. Mol. Biol. 371, 855–872 (2007)

    Article  CAS  Google Scholar 

  17. Bar-Nahum, G., Epshtein, V., Ruckenstein, A. E., Mustaev, A. & Nudler, E. A ratchet mechanism of transcription elongation and its control. Cell 120, 183–193 (2005)

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  19. Mentesana, P. E., Chin-Bow, S. T., Sousa, R. & McAllister, W. T. Characterization of halted T7 RNA polymerase elongation complexes reveals multiple factors that contribute to stability. J. Mol. Biol. 302, 1049–1062 (2000)

    Article  CAS  Google Scholar 

  20. 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)

    Article  CAS  Google Scholar 

  21. Wang, D., Bushnell, D. A., Westover, K. D., Kaplan, C. D. & Kornberg, R. D. Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis. Cell 127, 941–954 (2006)

    Article  CAS  Google Scholar 

  22. 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)

    Article  ADS  CAS  Google Scholar 

  23. Toulokhonov, I., Zhang, J., Palangat, M. & Landick, R. A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing. Mol. Cell 27, 406–419 (2007)

    Article  CAS  Google Scholar 

  24. Brennan, C. A., Dombroski, A. J. & Platt, T. Transcription termination factor rho is an RNA-DNA helicase. Cell 48, 945–952 (1987)

    Article  CAS  Google Scholar 

  25. Schwartz, A., Margeat, E., Rahmouni, A. R. & Boudvillain, M. Transcription termination factor rho can displace streptavidin from biotinylated RNA. J. Biol. Chem. 282, 1469–1476 (2007)

    Article  Google Scholar 

  26. Gusarov, I. & Nudler, E. The mechanism of intrinsic transcription termination. Mol. Cell 3, 495–504 (1999)

    Article  CAS  Google Scholar 

  27. Komissarova, N., Becker, J., Solter, S., Kireeva, M. & Kashlev, M. Shortening of RNA:DNA hybrid in the elongation complex of RNA polymerase is a prerequisite for transcription termination. Mol. Cell 10, 1151–1162 (2002)

    Article  CAS  Google Scholar 

  28. Epshtein, V., Cardinale, C., Ruckenstein, A., Borukhov, S. & Nudler, E. An allosteric path to transcription termination. Mol. Cell 28, 991–1001 (2007)

    Article  CAS  Google Scholar 

  29. Westover, K. D., Bushnell, D. A. & Kornberg, R. D. Structural basis of transcription: separation of RNA from DNA by RNA polymerase II. Science 303, 1014–1016 (2004)

    Article  ADS  CAS  Google Scholar 

  30. Naryshkina, T., Kuznedelov, K. & Severinov, K. The role of the largest RNA polymerase subunit lid element in preventing the formation of extended RNA-DNA hybrid. J. Mol. Biol. 361, 634–643 (2006)

    Article  CAS  Google Scholar 

  31. Nudler, E., Gusarov, I. & Bar-Nahum, G. Methods of walking with the RNA polymerase. Methods Enzymol. 371, 160–169 (2003)

    Article  CAS  Google Scholar 

  32. Wright, D. J., King, K. & Modrich, P. The negative charge of Glu-111 is required to activate the cleavage center of EcoRI endonuclease. J. Biol. Chem. 264, 11816–11821 (1989)

    CAS  PubMed  Google Scholar 

  33. Borukhov, S. & Goldfarb, A. Recombinant Escherichia coli RNA polymerase: purification of individually overexpressed subunits and in vitro assembly. Protein Expr. Purif. 4, 503–511 (1993)

    Article  CAS  Google Scholar 

  34. Nudler, E., Gusarov, I., Avetissova, E., Kozlov, M. & Goldfarb, A. Spatial organization of transcription elongation complex in Escherichia coli . Science 281, 424–428 (1998)

    Article  ADS  CAS  Google Scholar 

Download references

Acknowledgements

We thank I. Artsimovitch, S. Borukhov, K. Severinov, B. Stitt, D. Vassylyev and R. Weisberg for materials and discussions. This work was supported by a grant from the National Institutes of Health (R01GM58750, to E.N.).

Author Contributions V.E., D.D. and J.W. conducted the experimental work, discussed the results and commented on the manuscript. E.N. designed the study and wrote the paper.

Author information

Author notes

  1. Vitaly Epshtein and Dipak Dutta: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Biochemistry, New York University School of Medicine, New York, New York 10016, USA,

    Vitaly Epshtein, Dipak Dutta & Evgeny Nudler

  2. Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York 12201, USA,

    Joseph Wade

Authors
  1. Vitaly Epshtein
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Dipak Dutta
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Joseph Wade
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Evgeny Nudler
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Evgeny Nudler.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures, 1-11 with Legends and Supplementary Notes and Supplementary Methods. (PDF 1700 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Epshtein, V., Dutta, D., Wade, J. et al. An allosteric mechanism of Rho-dependent transcription termination. Nature 463, 245–249 (2010). https://doi.org/10.1038/nature08669

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature08669

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing