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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
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.
Varshavsky, A. (1996) The N-end rule: functions, mysteries, uses. Proc. Natl. Acad. Sci. USA 93, 12142–12149.
Bachmair, A. and Varshavsky, A. (1989) The degradation signal in a short-lived protein. Cell 56, 1019–1032.
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.
Bartel, B., Wnning, I., and Varshavsky, A. ((1990) The recognition component of the N-end rule pathway. EMBO J. 9, 3179–3189.
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.
Baumeister, W., Walz, J., Zuhl, F., and Seemuller, E. (1998) The proteasome: paradigm of a self-compartmentalizing protease. Cell 92, 367–380.
Thrower, J. S., Hoffman, L., Rechsteiner, M., and Pickart, C. M. (2000) Recognition of the polyubiquitin proteolytic signal. EMBO J. 19, 94–102.
Turner, G. C., Du, F., and Varshavsky, A. (2000) Peptides accelerate their uptake by activating a ubiquitin-dependent proteolytic pathway. Nature 405, 579–583.
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.
Varshavsky, A. (2000) Ubiquitin fusion technique and its descendants. Methods Enzymol. 327, 578–593.
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.
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.
Wilkinson, K. D. (1997) Regulation of ubiquitin-dependent processes by deubiquitinating enzymes. FASEB J. 11, 1245–1256.
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.
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.
Dohmen, R. J., Wu, P., and Varshavsky, A. (1994) Heat-inducible degron: a method for constructing temperature-sensitive mutants. Science 263, 1273–1276.
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.
Hardy, C. F. (1996) Characterization of an essential Orc2p-associated factor that plays a role in DNA replication. Mol. Cell. Biol. 16, 1832–1841.
Amon, A. (1997) Regulation of B-type cyclin proteolysis by Cdc28-associated kinases in budding yeast. EMBO J. 16, 2693–2702.
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.
Labib, K., Tercero, J. A., and Diffley, J. F. (2000) Uninterrupted MCM2-7 function required for DNA replication fork progression. Science 288, 1643–1647.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Petracek, M. E. and Longtine, M. S. (2002) PCR-based engineering of yeast genome. Methods Enzymol. 350, 445–469.
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.
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.
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.
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.
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.
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.
Madura, K., and Varshavsky, A. (1994) Degradation of G alpha by the N-end rule pathway. Science 265, 1454–1458.
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.
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.
Wach, A. (1996) PCR-synthesis of marker cassettes with long flanking homology regions for gene disruptions in S. cerevisiae. Yeast 12, 259–265.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights 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