Skip to main content

Inducible Degron and Its Application to Creating Conditional Mutants

  • Protocol
Yeast Protocol

Part of the book series: Methods in Molecular Biology ((MIMB,volume 313))

  • 6079 Accesses

Abstract

Conditional mutants are important tools particularly in the analysis of essential genes. In this chapter, a method is described that allows for a rapid design-based generation of temperature-sensitive alleles of many Saccharomyces cerevisiae genes. The method employs a temperature-inducible degron, denoted as td, which, when linked to the N-terminus of proteins to be studied, targets them for rapid degradation via the ubiquitin-dependent N-end rule pathway. Targeting, however, occurs only at elevated (restrictive) temperatures, whereas at lower (permissive) temperatures the degron is inactive. Strategies to generate td alleles are described, and the limitations of the method are discussed.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Bachmair, A., Finley, D., and Varshavsky, A. (1986) In vivo half-life of a protein is a function of its amino-terminal residue. Science 234, 179–186.

    Article  PubMed  CAS  Google Scholar 

  2. Varshavsky, A. (1996) The N-end rule: functions, mysteries, uses. Proc. Natl. Acad. Sci. USA 93, 12142–12149.

    Article  PubMed  CAS  Google Scholar 

  3. Bachmair, A. and Varshavsky, A. (1989) The degradation signal in a short-lived protein. Cell 56, 1019–1032.

    Article  PubMed  CAS  Google Scholar 

  4. Chau, V., Tobias, J. W., Bachmair, A., Marriott, D., Ecker, D. J., Gonda, D. K., and Varshavsky, A. (1989) A multiubiquitin chain is confined to specific lysine in a targeted short-lived protein. Science 243, 1576–1583.

    Article  PubMed  CAS  Google Scholar 

  5. Bartel, B., Wnning, I., and Varshavsky, A. ((1990) The recognition component of the N-end rule pathway. EMBO J. 9, 3179–3189.

    PubMed  CAS  Google Scholar 

  6. Dohmen, R. J., Madura, K., Bartel, B., and Varshavsky, A. (1991) The N-end rule is mediated by the UBC2(RAD6) ubiquitin-conjugating enzyme. Proc. Natl. Acad. Sci. USA 88, 7351–7355.

    Article  PubMed  CAS  Google Scholar 

  7. Baumeister, W., Walz, J., Zuhl, F., and Seemuller, E. (1998) The proteasome: paradigm of a self-compartmentalizing protease. Cell 92, 367–380.

    Article  PubMed  CAS  Google Scholar 

  8. Thrower, J. S., Hoffman, L., Rechsteiner, M., and Pickart, C. M. (2000) Recognition of the polyubiquitin proteolytic signal. EMBO J. 19, 94–102.

    Article  PubMed  CAS  Google Scholar 

  9. Turner, G. C., Du, F., and Varshavsky, A. (2000) Peptides accelerate their uptake by activating a ubiquitin-dependent proteolytic pathway. Nature 405, 579–583.

    Article  PubMed  CAS  Google Scholar 

  10. Rao, H., Uhlmann, F., Nasmyth, K., and Varshavsky, A. (2001) Degradation of a cohesin subunit by the N-end rule pathway is essential for chromosome stability. Nature 410, 955–959.

    Article  PubMed  CAS  Google Scholar 

  11. Varshavsky, A. (2000) Ubiquitin fusion technique and its descendants. Methods Enzymol. 327, 578–593.

    Article  PubMed  CAS  Google Scholar 

  12. Baker, R. T., Tobias, J. W., and Varshavsky, A. (1992) Ubiquitin-specific proteases of Saccharomyces cerevisiae. Cloning of UBP2 and UBP3, and functional analysis of the UBP gene family. J. Biol. Chem. 267, 23364–23375.

    PubMed  CAS  Google Scholar 

  13. Tobias, J. W. and Varshavsky, A. (1991) Cloning and functional analysis of the ubiquitin-specific protease gene UBP1 of Saccharomyces cerevisiae. J. Biol. Chem. 266, 12021–12028.

    PubMed  CAS  Google Scholar 

  14. Wilkinson, K. D. (1997) Regulation of ubiquitin-dependent processes by deubiquitinating enzymes. FASEB J. 11, 1245–1256.

    PubMed  CAS  Google Scholar 

  15. Park, E. C., Finley, D., and Szostak, J. W. (1992) A strategy for the generation of conditional mutations by protein destabilization. Proc. Natl. Acad. Sci. USA 89, 1249–1252.

    Article  PubMed  CAS  Google Scholar 

  16. Moqtaderi, Z., Bai, Y., Poon, D., Weil, P. A., and Struhl, K. (1996) TBP-associated factors are not generally required for transcriptional activation in yeast. Nature 383, 188–191.

    Article  PubMed  CAS  Google Scholar 

  17. Dohmen, R. J., Wu, P., and Varshavsky, A. (1994) Heat-inducible degron: a method for constructing temperature-sensitive mutants. Science 263, 1273–1276.

    Article  PubMed  CAS  Google Scholar 

  18. Levy, F., Johnston, J. A., and Varshavsky, A. (1999) Analysis of a conditional degradation signal in yeast and mammalian cells. Eur. J. Biochem. 259, 244–252.

    Article  PubMed  CAS  Google Scholar 

  19. Hardy, C. F. (1996) Characterization of an essential Orc2p-associated factor that plays a role in DNA replication. Mol. Cell. Biol. 16, 1832–1841.

    PubMed  CAS  Google Scholar 

  20. Amon, A. (1997) Regulation of B-type cyclin proteolysis by Cdc28-associated kinases in budding yeast. EMBO J. 16, 2693–2702.

    Article  PubMed  CAS  Google Scholar 

  21. Feaver, W. J., Huang, W., and Friedberg, E. C. (1999) The TFB4 subunit of yeast TFIIH is required for both nucleotide excision repair and RNA polymerase II transcription. J. Biol. Chem. 274, 29564–29567.

    Article  PubMed  CAS  Google Scholar 

  22. Labib, K., Tercero, J. A., and Diffley, J. F. (2000) Uninterrupted MCM2-7 function required for DNA replication fork progression. Science 288, 1643–1647.

    Article  PubMed  CAS  Google Scholar 

  23. Gardner, R. D., Poddar, A., Yellman, C., Tavormina, P. A., Monteagudo, M. C., and Burke, D. J. (2001) The spindle checkpoint of the yeast Saccharomyces cerevisiae requires kinetochore function and maps to the CBF3 domain. Genetics 157, 1493–1502.

    PubMed  CAS  Google Scholar 

  24. Cheeseman, I. M., Enquist-Newman, M., Muller-Reichert, T., Drubin, D. G., and Barnes, G. (2001) Mitotic spindle integrity and kinetochore function linked by the Duo1p/Dam1p complex. J. Cell Biol. 152, 197–212.

    Article  PubMed  CAS  Google Scholar 

  25. Zhang, Y., Yu, Z., Fu, X., and Liang, C. (2002) Noc3p, a bHLH protein, plays an integral role in the initiation of DNA replication in budding yeast. Cell 109, 849–860.

    Article  PubMed  CAS  Google Scholar 

  26. Kanemaki, M., Sanchez-Diaz, A., Gambus, A., and Labib, K. (2003) Functional proteomic identification of DNA replication proteins by induced proteolysis in vivo. Nature 423, 720–724.

    Article  PubMed  CAS  Google Scholar 

  27. Rajagopalan, S., Liling, Z., Liu, J., and Balasubramanian, M. (2004) The N-degron approach to create temperature-sensitive mutants in Schizosaccharomyces pombe. Methods 33, 206–212.

    Article  PubMed  CAS  Google Scholar 

  28. Tongaonkar, P., Beck, K., Shinde, U. P., and Madura, K. (1999) Characterization of a temperature-sensitive mutant of a ubiquitin-conjugating enzyme and its use as a heat-inducible degradation signal. Anal. Biochem. 272, 263–269.

    Article  PubMed  CAS  Google Scholar 

  29. Ghislain, M., Dohmen, R. J., Levy, F., and Varshavsky, A. (1996) Cdc48p interacts with Ufd3p, a WD repeat protein required for ubiquitin-mediated proteolysis in Saccharomyces cerevisiae. EMBO J. 15, 4884–4899.

    PubMed  CAS  Google Scholar 

  30. Gietz, R. D. and Sugino, A. (1988) New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. Gene 74, 527–534.

    Article  PubMed  CAS  Google Scholar 

  31. Sikorski, R. S. and Hieter, P. (1989) A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122, 19–27.

    PubMed  CAS  Google Scholar 

  32. Petracek, M. E. and Longtine, M. S. (2002) PCR-based engineering of yeast genome. Methods Enzymol. 350, 445–469.

    Article  PubMed  CAS  Google Scholar 

  33. Orr-Weaver, T. L., Szostak, J. W., and Rothstein, R. J. (1981) Yeast transformation: a model system for the study of recombination. Proc. Natl. Acad. Sci. USA 78, 6354–6358.

    Article  PubMed  CAS  Google Scholar 

  34. Baudin, A., Ozier-Kalogeropoulos, O., Denouel, A., Lacroute, F., and Cullin, C. (1993) A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. Nucleic Acids Res. 21, 3329–3330.

    Article  PubMed  CAS  Google Scholar 

  35. Manivasakam, P., Weber, S. C., McElver, J., and Schiestl, R. H. (1995) Microhomology mediated PCR targeting in Saccharomyces cerevisiae. Nucleic Acids Res. 23, 2799–2800.

    Article  PubMed  CAS  Google Scholar 

  36. Lorenz, M. C., Muir, R. S., Lim, E., McElver, J., Weber, S. C., and Heitman, J. (1995) Gene disruption with PCR products in Saccharomyces cerevisiae. Gene 158, 113–117.

    Article  PubMed  CAS  Google Scholar 

  37. Wach, A., Brachat, A., Pohlmann, R., and Philippsen, P. (1994) New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae. Yeast 10, 1793–1808.

    Article  PubMed  CAS  Google Scholar 

  38. Dohmen, R. J., Strasser, A. W., Höner, C. B., and Hollenberg, C. P. (1991) An efficient transformation procedure enabling long-term storage of competent cells of various yeast genera. Yeast 7, 691–692.

    Article  PubMed  CAS  Google Scholar 

  39. Madura, K., and Varshavsky, A. (1994) Degradation of G alpha by the N-end rule pathway. Science 265, 1454–1458.

    Article  PubMed  CAS  Google Scholar 

  40. Gosink, M. M., and Vierstra, R. D. (1995) Redirecting the specificity of ubiquitination by modifying ubiquitin-conjugating enzymes. Proc. Natl. Acad. Sci. USA 92, 9117–9121.

    Article  PubMed  CAS  Google Scholar 

  41. Zhou, P., Bogacki, R., McReynolds, L., and Howley, P. M. (2000) Harnessing the ubiquitination machinery to target the degradation of specific cellular proteins. Mol. Cell 6, 751–756.

    Article  PubMed  CAS  Google Scholar 

  42. Wach, A. (1996) PCR-synthesis of marker cassettes with long flanking homology regions for gene disruptions in S. cerevisiae. Yeast 12, 259–265.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2006 Humana Press Inc., Totowa, NJ

About this protocol

Cite this protocol

Dohmen, R.J. (2006). Inducible Degron and Its Application to Creating Conditional Mutants. In: Xiao, W. (eds) Yeast Protocol. Methods in Molecular Biology, vol 313. Humana Press, Totowa, NJ. https://doi.org/10.1385/1-59259-958-3:145

Download citation

  • DOI: https://doi.org/10.1385/1-59259-958-3:145

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-58829-437-1

  • Online ISBN: 978-1-59259-958-5

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics