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Frontiers of protein expression control with conditional degrons

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Abstract

It is useful to artificially control the expression levels of a protein of interest (POI), not only for its characterization in vivo, but also for the modulation of biological pathways. Overexpression of a POI is relatively easy because it is possible to drive its expression from a transgene encoding the POI under the control of a strong promoter. However, it is more challenging to reduce or deplete the expression of a POI. A protein domain called “degron”, which induces rapid proteolysis by the proteasome, can be used for this purpose. Degron-based technologies for the conditional depletion of POI—degron fusion proteins have been developed by exploiting various pathways leading to proteasomal degradation. Compared with other depletion technologies that control the expression levels of POIs at the DNA or mRNA levels, these protein-depletion approaches are advantageous in terms of specificity, reversibility, and the time required for depletion. Current conditional degron-based technologies are described and discussed.

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References

  1. Armstrong CM, Goldberg DE (2007) An FKBP destabilization domain modulates protein levels in Plasmodium falciparum. Nat Methods 4:1007–1009. doi:10.1038/nmeth1132

    Article  PubMed  CAS  Google Scholar 

  2. Banaszynski LA, Chen LC, Maynard-Smith LA, Ooi AG, Wandless TJ (2006) A rapid, reversible, and tunable method to regulate protein function in living cells using synthetic small molecules. Cell 126:995–1004. doi:10.1016/j.cell.2006.07.025

    Article  PubMed  CAS  Google Scholar 

  3. Banaszynski LA, Sellmyer MA, Contag CH, Wandless TJ, Thorne SH (2008) Chemical control of protein stability and function in living mice. Nat Med 14:1123–1127. doi:10.1038/nm.1754

    Article  PubMed  CAS  Google Scholar 

  4. Bonger KM, Chen LC, Liu CW, Wandless TJ (2011) Small-molecule displacement of a cryptic degron causes conditional protein degradation. Nat Chem Biol 7:531–537. doi:10.1038/nchembio.598

    Article  PubMed  CAS  Google Scholar 

  5. Buchberger A, Bukau B, Sommer T (2010) Protein quality control in the cytosol and the endoplasmic reticulum: brothers in arms. Mol Cell 40:238–252. doi:10.1016/j.molcel.2010.10.001

    Article  PubMed  CAS  Google Scholar 

  6. Dharmasiri N, Dharmasiri S, Estelle M (2005) The F-box protein TIR1 is an auxin receptor. Nature 435:441–445. doi:10.1038/nature03543

    Article  PubMed  CAS  Google Scholar 

  7. Dharmasiri N, Dharmasiri S, Weijers D, Lechner E, Yamada M, Hobbie L, Ehrismann JS, Jurgens G, Estelle M (2005) Plant development is regulated by a family of auxin receptor F box proteins. Dev Cell 9:109–119. doi:10.1016/j.devcel.2005.05.014

    Article  PubMed  CAS  Google Scholar 

  8. Dohmen RJ, Varshavsky A (2005) Heat-inducible degron and the making of conditional mutants. Methods Enzymol 399:799–822. doi:10.1016/S0076-6879(05)99052-6

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  10. Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411:494–498. doi:10.1038/35078107

    Article  PubMed  CAS  Google Scholar 

  11. Gossen M, Bujard H (1992) Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. Proc Natl Acad Sci USA 89:5547–5551

    Article  PubMed  CAS  Google Scholar 

  12. Gregan J, Lindner K, Brimage L, Franklin R, Namdar M, Hart EA, Aves SJ, Kearsey SE (2003) Fission yeast Cdc23/Mcm10 functions after pre-replicative complex formation to promote Cdc45 chromatin binding. Mol Biol Cell 14:3876–3887. doi:10.1091/mbc.E03-02-0090

    Article  PubMed  CAS  Google Scholar 

  13. Gronemeyer T, Godin G, Johnsson K (2005) Adding value to fusion proteins through covalent labelling. Curr Opin Biotechnol 16:453–458. doi:10.1016/j.copbio.2005.06.001

    Article  PubMed  CAS  Google Scholar 

  14. Herm-Gotz A, Agop-Nersesian C, Munter S, Grimley JS, Wandless TJ, Frischknecht F, Meissner M (2007) Rapid control of protein level in the apicomplexan Toxoplasma gondii. Nat Methods 4:1003–1005. doi:10.1038/nmeth1134

    Article  PubMed  Google Scholar 

  15. Iwamoto M, Bjorklund T, Lundberg C, Kirik D, Wandless TJ (2010) A general chemical method to regulate protein stability in the mammalian central nervous system. Chem Biol 17:981–988. doi:10.1016/j.chembiol.2010.07.009

    Article  PubMed  CAS  Google Scholar 

  16. Jungbluth M, Renicke C, Taxis C (2010) Targeted protein depletion in Saccharomyces cerevisiae by activation of a bidirectional degron. BMC Syst Biol 4:176. doi:10.1186/1752-0509-4-176

    Article  PubMed  CAS  Google Scholar 

  17. Kanemaki M, Sanchez-Diaz A, Gambus A, Labib K (2003) Functional proteomic identification of DNA replication proteins by induced proteolysis in vivo. Nature 423:720–724. doi:10.1038/nature01692

    Article  PubMed  CAS  Google Scholar 

  18. Kanke M, Nishimura K, Kanemaki M, Kakimoto T, Takahashi TS, Nakagawa T, Masukata H (2011) Auxin-inducible protein depletion system in fission yeast. BMC Cell Biol 12:8. doi:10.1186/1471-2121-12-8

    Article  PubMed  CAS  Google Scholar 

  19. Kearsey SE, Gregan J (2009) Using the DHFR heat-inducible degron for protein inactivation in Schizosaccharomyces pombe. Methods Mol Biol 521:483–492

    Article  PubMed  CAS  Google Scholar 

  20. Labib K, Tercero JA, Diffley JF (2000) Uninterrupted MCM2-7 function required for DNA replication fork progression. Science 288:1643–1647

    Article  PubMed  CAS  Google Scholar 

  21. Lindner K, Gregan J, Montgomery S, Kearsey SE (2002) Essential role of MCM proteins in premeiotic DNA replication. Mol Biol Cell 13:435–444. doi:10.1091/mbc.01-11-0537

    Article  PubMed  CAS  Google Scholar 

  22. Los GV, Wood K (2007) The HaloTag: a novel technology for cell imaging and protein analysis. Methods Mol Biol 356:195–208

    PubMed  CAS  Google Scholar 

  23. Miller LW, Cai Y, Sheetz MP, Cornish VW (2005) In vivo protein labeling with trimethoprim conjugates: a flexible chemical tag. Nat Methods 2:255–257. doi:10.1038/nmeth749

    Article  PubMed  CAS  Google Scholar 

  24. Miller JC, Tan S, Qiao G, Barlow KA, Wang J, Xia DF, Meng X, Paschon DE, Leung E, Hinkley SJ, Dulay GP, Hua KL, Ankoudinova I, Cost GJ, Urnov FD, Zhang HS, Holmes MC, Zhang L, Gregory PD, Rebar EJ (2011) A TALE nuclease architecture for efficient genome editing. Nat Biotechnol 29:143–148. doi:10.1038/nbt.1755

    Article  PubMed  CAS  Google Scholar 

  25. Neklesa TK, Tae HS, Schneekloth AR, Stulberg MJ, Corson TW, Sundberg TB, Raina K, Holley SA, Crews CM (2011) Small-molecule hydrophobic tagging-induced degradation of HaloTag fusion proteins. Nat Chem Biol 7:538–543. doi:10.1038/nchembio.597

    Article  PubMed  CAS  Google Scholar 

  26. Nishimura K, Fukagawa T, Takisawa H, Kakimoto T, Kanemaki M (2009) An auxin-based degron system for the rapid depletion of proteins in nonplant cells. Nat Methods 6:917–922. doi:10.1038/nmeth.1401

    Article  PubMed  CAS  Google Scholar 

  27. Porteus M (2008) Design and testing of zinc finger nucleases for use in mammalian cells. Methods Mol Biol 435:47–61. doi:10.1007/978-1-59745-232-8_4

    Article  PubMed  CAS  Google Scholar 

  28. Rajagopalan S, Liling Z, Liu J, Balasubramanian M (2004) The N-degron approach to create temperature-sensitive mutants in Schizosaccharomyces pombe. Methods 33:206–212. doi:10.1016/j.ymeth.2003.11.015

    Article  PubMed  CAS  Google Scholar 

  29. Rakhit R, Edwards SR, Iwamoto M, Wandless TJ (2011) Evaluation of FKBP and DHFR based destabilizing domains in Saccharomyces cerevisiae. Bioorg Med Chem Lett 21:4965–4968. doi:10.1016/j.bmcl.2011.06.006

    Article  PubMed  CAS  Google Scholar 

  30. Sakamoto KM, Kim KB, Kumagai A, Mercurio F, Crews CM, Deshaies RJ (2001) Protacs: chimeric molecules that target proteins to the Skp1-Cullin-F box complex for ubiquitination and degradation. Proc Natl Acad Sci USA 98:8554–8559. doi:10.1073/pnas.141230798

    Article  PubMed  CAS  Google Scholar 

  31. Sanchez-Diaz A, Kanemaki M, Marchesi V, Labib K (2004) Rapid depletion of budding yeast proteins by fusion to a heat-inducible degron. Sci STKE PL8. doi:10.1126/stke.2232004pl8

  32. Sanchez-Diaz A, Marchesi V, Murray S, Jones R, Pereira G, Edmondson R, Allen T, Labib K (2008) Inn1 couples contraction of the actomyosin ring to membrane ingression during cytokinesis in budding yeast. Nat Cell Biol 10:395–406. doi:10.1038/ncb1701

    Article  PubMed  CAS  Google Scholar 

  33. Sauer B, Henderson N (1988) Site-specific DNA recombination in mammalian cells by the Cre recombinase of bacteriophage P1. Proc Natl Acad Sci USA 85:5166–5170

    Article  PubMed  CAS  Google Scholar 

  34. Schneekloth JS Jr, Fonseca FN, Koldobskiy M, Mandal A, Deshaies R, Sakamoto K, Crews CM (2004) Chemical genetic control of protein levels: selective in vivo targeted degradation. J Am Chem Soc 126:3748–3754. doi:10.1021/ja039025z

    Article  PubMed  CAS  Google Scholar 

  35. Sriram SM, Kim BY, Kwon YT (2011) The N-end rule pathway: emerging functions and molecular principles of substrate recognition. Nat Rev Mol Cell Biol 12:735–747. doi:10.1038/nrm3217

    Article  PubMed  CAS  Google Scholar 

  36. Su X, Bernal JA, Venkitaraman AR (2008) Cell-cycle coordination between DNA replication and recombination revealed by a vertebrate N-end rule degron-Rad51. Nat Struct Mol Biol 15:1049–1058. doi:10.1038/nsmb.1490

    Article  PubMed  CAS  Google Scholar 

  37. Suzuki T, Varshavsky A (1999) Degradation signals in the lysine-asparagine sequence space. EMBO J 18:6017–6026. doi:10.1093/emboj/18.21.6017

    Article  PubMed  CAS  Google Scholar 

  38. Tan X, Calderon-Villalobos LI, Sharon M, Zheng C, Robinson CV, Estelle M, Zheng N (2007) Mechanism of auxin perception by the TIR1 ubiquitin ligase. Nature 446:640–645. doi:10.1038/nature05731

    Article  PubMed  CAS  Google Scholar 

  39. Taxis C, Knop M (2012) TIPI: TEV protease-mediated induction of protein instability. Methods Mol Biol 832:611–626. doi:10.1007/978-1-61779-474-2_43

    Article  PubMed  CAS  Google Scholar 

  40. Taxis C, Stier G, Spadaccini R, Knop M (2009) Efficient protein depletion by genetically controlled deprotection of a dormant N-degron. Mol Syst Biol 5:267. doi:10.1038/msb.2009.25

    Article  PubMed  Google Scholar 

  41. Urnov FD, Rebar EJ, Holmes MC, Zhang HS, Gregory PD (2010) Genome editing with engineered zinc finger nucleases. Nat Rev Genet 11:636–646. doi:10.1038/nrg2842

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  43. Watase G, Takisawa H, Kanemaki MT (2012) Mcm10 plays a role in functioning of the eukaryotic replicative DNA helicase, Cdc45-Mcm-GINS. Curr Biol 22:343–349. doi:10.1016/j.cub.2012.01.023

    Article  PubMed  CAS  Google Scholar 

  44. Zhou P (2005) Targeted protein degradation. Curr Opin Chem Biol 9:51–55. doi:10.1016/j.cbpa.2004.10.012

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

The author’s research discussed in this review was supported by a Grant-in-Aid for Young Scientists (A) and a Challenging Exploratory Research Grant from the Ministry of Education, Science, Sports and Culture of Japan.

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Correspondence to Masato T. Kanemaki.

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This article is a submission for the Special Issue of “Recent Advances in Tools for Measuring and Manipulating Biochemical Signals and Mechanical Forces in Living Cells”.

This article is published as part of the Special Issue on “Molecular Sensors”

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Kanemaki, M.T. Frontiers of protein expression control with conditional degrons. Pflugers Arch - Eur J Physiol 465, 419–425 (2013). https://doi.org/10.1007/s00424-012-1203-y

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  • DOI: https://doi.org/10.1007/s00424-012-1203-y

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