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
Armstrong CM, Goldberg DE (2007) An FKBP destabilization domain modulates protein levels in Plasmodium falciparum. Nat Methods 4:1007–1009. doi:10.1038/nmeth1132
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
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
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
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
Dharmasiri N, Dharmasiri S, Estelle M (2005) The F-box protein TIR1 is an auxin receptor. Nature 435:441–445. doi:10.1038/nature03543
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
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
Dohmen RJ, Wu P, Varshavsky A (1994) Heat-inducible degron: a method for constructing temperature-sensitive mutants. Science 263:1273–1276
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
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
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
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
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
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
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
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
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
Kearsey SE, Gregan J (2009) Using the DHFR heat-inducible degron for protein inactivation in Schizosaccharomyces pombe. Methods Mol Biol 521:483–492
Labib K, Tercero JA, Diffley JF (2000) Uninterrupted MCM2-7 function required for DNA replication fork progression. Science 288:1643–1647
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
Los GV, Wood K (2007) The HaloTag: a novel technology for cell imaging and protein analysis. Methods Mol Biol 356:195–208
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Varshavsky A (1996) The N-end rule: functions, mysteries, uses. Proc Natl Acad Sci USA 93:12142–12149
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
Zhou P (2005) Targeted protein degradation. Curr Opin Chem Biol 9:51–55. doi:10.1016/j.cbpa.2004.10.012
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
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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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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