Synthetic biology approaches for targeted protein degradation
Tài liệu tham khảo
Ariotti, 2018, Ultrastructural localisation of protein interactions using conditionally stable nanobodies, PLoS Biol., 16, 10.1371/journal.pbio.2005473
Bachmair, 1989, The degradation signal in a short-lived protein, Cell, 56, 1019, 10.1016/0092-8674(89)90635-1
Bachmair, 1986, In vivo half-life of a protein is a function of its amino-terminal residue, Science, 234, 179, 10.1126/science.3018930
Baltz, 2018, Design and functional characterization of synthetic E3 ubiquitin ligases for targeted protein depletion, Curr. Protoc. Chem. Biol., 10, 72, 10.1002/cpch.37
Banaszynski, 2006, A rapid, reversible, and tunable method to regulate protein function in living cells using synthetic small molecules, Cell, 126, 995, 10.1016/j.cell.2006.07.025
Berndsen, 2014, New insights into ubiquitin E3 ligase mechanism, Nat. Struct. Mol. Biol., 21, 301, 10.1038/nsmb.2780
Bonger, 2011, Small-molecule displacement of a cryptic degron causes conditional protein degradation, Nat. Chem. Biol., 7, 531, 10.1038/nchembio.598
Budenholzer, 2017, Proteasome structure and assembly, J. Mol. Biol., 429, 3500, 10.1016/j.jmb.2017.05.027
Caussinus, 2011, Fluorescent fusion protein knockout mediated by anti-GFP nanobody, Nat. Struct. Mol. Biol., 19, 117, 10.1038/nsmb.2180
Chassin, 2019, A modular degron library for synthetic circuits in mammalian cells, Nat. Commun., 10, 2013, 10.1038/s41467-019-09974-5
Chau, 1989, A multiubiquitin chain is confined to specific lysine in a targeted short-lived protein, Science, 243, 1576, 10.1126/science.2538923
Chung, 2015, Tunable and reversible drug control of protein production via a self-excising degron, Nat. Chem. Biol., 11, 713, 10.1038/nchembio.1869
Clift, 2017, A method for the acute and rapid degradation of endogenous proteins, Cell, 171, 1692, 10.1016/j.cell.2017.10.033
Collins, 2017, The logic of the 26S proteasome, Cell, 169, 792, 10.1016/j.cell.2017.04.023
Collins, 2017, Chemical approaches to targeted protein degradation through modulation of the ubiquitin–proteasome pathway, Biochem. J., 474, 1127, 10.1042/BCJ20160762
Davey, 2016, Building a regulatory network with short linear sequence motifs: lessons from the degrons of the anaphase-promoting complex, Mol. Cell, 64, 12, 10.1016/j.molcel.2016.09.006
Delacour, 2015, Light-activated proteolysis for the spatiotemporal control of proteins, ACS Chem. Biol., 10, 1643, 10.1021/acschembio.5b00069
Deshaies, 2009, RING domain E3 ubiquitin ligases, Annu. Rev. Biochem., 78, 399, 10.1146/annurev.biochem.78.101807.093809
Dharmasiri, 2005, The F-box protein TIR1 is an auxin receptor, Nature, 435, 441, 10.1038/nature03543
Dikic, 2018, Mechanism and medical implications of mammalian autophagy, Nat. Rev. Mol. Cell Biol., 19, 349, 10.1038/s41580-018-0003-4
Dohmen, 1994, Heat-inducible degron: a method for constructing temperature-sensitive mutants, Science, 263, 1273, 10.1126/science.8122109
Duda, 2013, Structure of HHARI, a RING-IBR-RING ubiquitin ligase: autoinhibition of an Ariadne-family E3 and insights into ligation mechanism, Structure, 21, 1030, 10.1016/j.str.2013.04.019
Erales, 2014, Ubiquitin-independent proteasomal degradation, Biochim. Biophys. Acta, Mol. Cell Res., 1843, 216, 10.1016/j.bbamcr.2013.05.008
Faden, 2016, Phenotypes on demand via switchable target protein degradation in multicellular organisms, Nat. Commun., 7, 10.1038/ncomms12202
Feldman, 1997, A complex of Cdc4p, Skp1p, and Cdc53p/cullin catalyzes ubiquitination of the phosphorylated CDK inhibitor Sic1p, Cell, 91, 221, 10.1016/S0092-8674(00)80404-3
Fernandez-Rodriguez, 2016, Post-translational control of genetic circuits using Potyvirus proteases, Nucleic Acids Res., 44, 6493, 10.1093/nar/gkw537
Fulcher, 2016, An affinity-directed protein missile system for targeted proteolysis, Open Biol., 6, 10.1098/rsob.160255
Fulcher, 2017, Targeting endogenous proteins for degradation through the affinity-directed protein missile system, Open Biol., 7, 10.1098/rsob.170066
Gao, 2018, Programmable protein circuits in living cells, Science, 361, 1252, 10.1126/science.aat5062
Gaynor, 2017, Induced prodrug activation by conditional protein degradation, J. Biotechnol., 260, 62, 10.1016/j.jbiotec.2017.09.005
Goglia, 2019, A bright future: optogenetics to dissect the spatiotemporal control of cell behavior, Curr. Opin. Chem. Biol., 48, 106, 10.1016/j.cbpa.2018.11.010
Gross, 2016, An E3-ligase-based method for ablating inhibitory synapses, Nat. Methods, 13, 673, 10.1038/nmeth.3894
Gu, 2018, PROTACs: an emerging targeting technique for protein degradation in drug discovery, BioEssays, 40, 10.1002/bies.201700247
Harashima, 2013, Cell cycle control across the eukaryotic kingdom, Trends Cell Biol., 23, 345, 10.1016/j.tcb.2013.03.002
Harper, 2002, The anaphase-promoting complex: it’s not just for mitosis any more, Genes Dev., 16, 2179, 10.1101/gad.1013102
Harper, 2003, Structural basis of a phototropin light switch, Science, 301, 1541, 10.1126/science.1086810
Hassanzadeh-Ghassabeh, 2013, Nanobodies and their potential applications, Nanomedicine, 8, 1013, 10.2217/nnm.13.86
Hatakeyama, 2005, Targeted destruction of c-Myc by an engineered ubiquitin ligase suppresses cell transformation and tumor formation, Cancer Res., 65, 7874, 10.1158/0008-5472.CAN-05-1581
Holland, 2012, Inducible, reversible system for the rapid and complete degradation of proteins in mammalian cells, Proc. Natl. Acad. Sci., 109, E3350, 10.1073/pnas.1216880109
Holst, 2006, Rapid analysis of T-cell selection in vivo using T cell-receptor retrogenic mice
Hsieh, 2009, Construction of mutant TKGFP for real-time imaging of temporal dynamics of HIF-1 signal transduction activity mediated by hypoxia and Reoxygenation in tumors in living mice, J. Nucl. Med., 50, 2049, 10.2967/jnumed.108.061234
Huang, 1999, Structure of an E6AP-UbcH7 complex: insights into ubiquitination by the E2-E3 enzyme cascade, Science, 286, 1321, 10.1126/science.286.5443.1321
Hwang, 2008, Regulation of peptide import through phosphorylation of Ubr1, the ubiquitin ligase of the N-end rule pathway, Proc. Natl. Acad. Sci., 105, 19188, 10.1073/pnas.0808891105
Hwang, 2010, N-terminal acetylation of cellular proteins creates specific degradation signals, Science, 327, 973, 10.1126/science.1183147
Iwamoto, 2010, A general chemical method to regulate protein stability in the mammalian central nervous system, Chem. Biol., 17, 981, 10.1016/j.chembiol.2010.07.009
James, 2007, Structural basis for PRYSPRY-mediated tripartite motif (TRIM) protein function, Proc. Natl. Acad. Sci., 104, 6200, 10.1073/pnas.0609174104
Jin, 2004, Systematic analysis and nomenclature of mammalian F-box proteins, Genes Dev., 18, 2573, 10.1101/gad.1255304
Joshi, 2015, Engineering degrons of yeast ornithine decarboxylase as vehicles for efficient targeted protein degradation, Biochim. Biophys. Acta, Gen. Subj., 1850, 2452, 10.1016/j.bbagen.2015.09.003
Jungbluth, 2010, Targeted protein depletion in Saccharomyces cerevisiae by activation of a bidirectional degron, BMC Syst. Biol., 4, 176, 10.1186/1752-0509-4-176
Kamadurai, 2009, Insights into ubiquitin transfer cascades from a structure of a UbcH5B~Ubiquitin-HECTNEDD4L complex, Mol. Cell, 36, 1095, 10.1016/j.molcel.2009.11.010
Kanner, 2017, Sculpting ion channel functional expression with engineered ubiquitin ligases, Elife, 6, 10.7554/eLife.29744
Kawano, 2017, Switching with red and blue, Nat. Chem. Biol., 13, 573, 10.1038/nchembio.2387
Kearsey, 2009, Using the DHFR heat-inducible degron for protein inactivation in schizosaccharomyces pombe, Methods in Mol. Biol. (Clifton, N.J.), 483, 10.1007/978-1-60327-815-7_27
Kepinski, 2005, The Arabidopsis F-box protein TIR1 is an auxin receptor, Nature, 435, 446, 10.1038/nature03542
Kim, 2017, Integration of optogenetics with complementary methodologies in systems neuroscience, Nat. Rev. Neurosci., 18, 222, 10.1038/nrn.2017.15
Komander, 2012, The ubiquitin code, Annu. Rev. Biochem., 81, 203, 10.1146/annurev-biochem-060310-170328
Kong, 2014, Engineering a single ubiquitin ligase for the selective degradation of all activated ErbB receptor tyrosine kinases, Oncogene, 33, 986, 10.1038/onc.2013.33
Lai, 2017, Induced protein degradation: an emerging drug discovery paradigm, Nat. Rev. Drug Discov., 16, 101, 10.1038/nrd.2016.211
Lau, 2010, Precise control of protein concentration in living cells, Angew. Chem. Int. Ed., 49, 8458, 10.1002/anie.201003073
Lemmens, 2018, DNA replication determines timing of mitosis by restricting CDK1 and PLK1 activation, Mol. Cell, 71, 117, 10.1016/j.molcel.2018.05.026
Levine, 2019, Biological functions of autophagy genes: a disease perspective, Cell, 176, 11, 10.1016/j.cell.2018.09.048
Li, 1998, Generation of destabilized green fluorescent protein as a transcription reporter, J. Biol. Chem., 273, 34970, 10.1074/jbc.273.52.34970
Lieser, 2019, Controlled epidermal growth factor receptor ligand display on cancer suicide enzymes via unnatural amino acid engineering for enhanced intracellular delivery in breast cancer cells, Bioconjug. Chem., 30, 432, 10.1021/acs.bioconjchem.8b00783
Lin, 2014, A dual small-molecule rheostat for precise control of protein concentration in mammalian cells, ChemBioChem, 15, 805, 10.1002/cbic.201400006
Liu, 2017, Identification of new degrons in streptococcus mutans reveals a novel strategy for engineering targeted, controllable proteolysis, Front. Microbiol., 8, 10.3389/fmicb.2017.02572
Liu, 2018, Programming bacteria with light—sensors and applications in synthetic biology, Front. Microbiol., 9, 10.3389/fmicb.2018.02692
Lorick, 1999, RING fingers mediate ubiquitin-conjugating enzyme (E2)-dependent ubiquitination, Proc. Natl. Acad. Sci. U. S. A., 96, 11364, 10.1073/pnas.96.20.11364
Ludwicki, 2019, Broad-Spectrum proteome editing with an engineered bacterial ubiquitin ligase mimic, ACS Cent. Sci., 5, 10.1021/acscentsci.9b00127
Lydeard, 2013, Building and remodelling Cullin-RING E3 ubiquitin ligases, EMBO Rep., 14, 1050, 10.1038/embor.2013.173
Mallery, 2010, Antibodies mediate intracellular immunity through tripartite motif-containing 21 (TRIM21), Proc. Natl. Acad. Sci., 107, 19985, 10.1073/pnas.1014074107
Metzger, 2012, HECT and RING finger families of E3 ubiquitin ligases at a glance, J. Cell Sci., 125, 531, 10.1242/jcs.091777
Morgan, 1997, Cyclin-dependent kinases: engines, clocks, and microprocessors, Annu. Rev. Cell Dev. Biol., 13, 261, 10.1146/annurev.cellbio.13.1.261
Mullard, 2019, First targeted protein degrader hits the clinic, Nat. Rev. Drug Discov., 18, 237
Murakami, 1992, Ornithine decarboxylase is degraded by the 26S proteasome without ubiquitination, Nature, 360, 597, 10.1038/360597a0
Natsume, 2017, Conditional degrons for controlling protein expression at the protein level, Annu. Rev. Genet., 51, 83, 10.1146/annurev-genet-120116-024656
Nishimura, 2009, An auxin-based degron system for the rapid depletion of proteins in nonplant cells, Nat. Methods, 6, 917, 10.1038/nmeth.1401
Ochoa-Fernandez, 2016, Optogenetics in plants: red/far-red light control of gene expression, 125, 10.1007/978-1-4939-3512-3_9
Portnoff, 2014, Ubiquibodies, synthetic E3 ubiquitin ligases endowed with unnatural substrate specificity for targeted protein silencing, J. Biol. Chem., 289, 7844, 10.1074/jbc.M113.544825
Prakash, 2009, Substrate selection by the proteasome during degradation of protein complexes, Nat. Chem. Biol., 5, 29, 10.1038/nchembio.130
Pratt, 2007, Small-molecule-mediated rescue of protein function by an inducible proteolytic shunt, Proc. Natl. Acad. Sci., 104, 11209, 10.1073/pnas.0700816104
Renicke, 2013, A LOV2 domain-based optogenetic tool to control protein degradation and cellular function, Chem. Biol., 20, 619, 10.1016/j.chembiol.2013.03.005
Saeki, 2017, Ubiquitin recognition by the proteasome, J. Biochem., 161
Sakamoto, 2001, Protacs: chimeric molecules that target proteins to the Skp1-Cullin-F box complex for ubiquitination and degradation, Proc. Natl. Acad. Sci., 98, 8554, 10.1073/pnas.141230798
Satyanarayana, 2009, Mammalian cell-cycle regulation: several Cdks, numerous cyclins and diverse compensatory mechanisms, Oncogene, 28, 2925, 10.1038/onc.2009.170
Schmit, 2019, Targeted protein degradation through cytosolic delivery of Monobody binders using bacterial toxins, ACS Chem. Biol., 14, 916, 10.1021/acschembio.9b00113
Schrader, 2009, Targeting proteins for degradation, Nat. Chem. Biol., 5, 815, 10.1038/nchembio.250
Sherr, 1999, CDK inhibitors: positive and negative regulators of G1-phase progression, Genes Dev., 13, 1501, 10.1101/gad.13.12.1501
Skaar, 2009, SnapShot: F box proteins II, Cell, 137, 1358.e1, 10.1016/j.cell.2009.05.040
Skaar, 2009, SnapShot: F box proteins I, Cell, 137, 1160, 10.1016/j.cell.2009.05.039
Skaar, 2013, Mechanisms and function of substrate recruitment by F-box proteins, Nat. Rev. Mol. Cell Biol., 14, 369, 10.1038/nrm3582
Skowyra, 1997, F-box proteins are receptors that recruit phosphorylated substrates to the SCF ubiquitin-ligase complex, Cell, 91, 209, 10.1016/S0092-8674(00)80403-1
Su, 2008, Cell-cycle coordination between DNA replication and recombination revealed by a vertebrate N-end rule degron-Rad51, Nat. Struct. Mol. Biol., 15, 1049, 10.1038/nsmb.1490
Szymczak, 2004, Correction of multi-gene deficiency in vivo using a single “self-cleaving” 2A peptide-based retroviral vector, Nat. Biotechnol., 22, 589, 10.1038/nbt957
Tan, 2007, Mechanism of auxin perception by the TIR1 ubiquitin ligase, Nature, 446, 640, 10.1038/nature05731
Tang, 2016, Detection and manipulation of live antigen-expressing cells using conditionally stable nanobodies, Elife, 5, 10.7554/eLife.15312
Tasaki, 2009, The substrate recognition domains of the N-end rule pathway, J. Biol. Chem., 284, 1884, 10.1074/jbc.M803641200
Taxis, 2009, Efficient protein depletion by genetically controlled deprotection of a dormant N-degron, Mol. Syst. Biol., 5, 267, 10.1038/msb.2009.25
Toure, 2016, Small-molecule PROTACS: new approaches to protein degradation, Angew. Chem. Int. Ed., 55, 1966, 10.1002/anie.201507978
Van Audenhove, 2013, Mapping cytoskeletal protein function in cells by means of nanobodies, Cytoskeleton, 70, 604, 10.1002/cm.21122
Varshavsky, 1996, The N-end rule: functions, mysteries, uses, Proc. Natl. Acad. Sci. U. S. A., 93, 12142, 10.1073/pnas.93.22.12142
Varshavsky, 2005, Ubiquitin fusion technique and related methods, Methods Enzymol., 777, 10.1016/S0076-6879(05)99051-4
Varshavsky, 2011, The N-end rule pathway and regulation by proteolysis, Protein Sci., 20, 1298, 10.1002/pro.666
Wenzel, 2011, UBCH7 reactivity profile reveals parkin and HHARI to be RING/HECT hybrids, Nature, 474, 105, 10.1038/nature09966
Wilkinson, 2000, Ubiquitination and deubiquitination: targeting of proteins for degradation by the proteasome, Semin. Cell Dev. Biol., 11, 141, 10.1006/scdb.2000.0164
Xia, 2008, Substrate-binding sites of UBR1, the ubiquitin ligase of the N-end rule pathway, J. Biol. Chem., 283, 24011, 10.1074/jbc.M802583200
Xie, 1999, The E2-E3 interaction in the N-end rule pathway: the RING-H2 finger of E3 is required for the synthesis of multiubiquitin chain, EMBO J., 18, 6832, 10.1093/emboj/18.23.6832
Yan, 2015, Replication-competent influenza virus and respiratory syncytial virus luciferase reporter strains engineered for co-infections identify antiviral compounds in combination screens, Biochemistry, 54, 5589, 10.1021/acs.biochem.5b00623
Yu, 2017, Recognition of client proteins by the proteasome, Annu. Rev. Biophys., 46, 149, 10.1146/annurev-biophys-070816-033719
Yu, 2015, Pac-man for biotechnology: co-opting degrons for targeted protein degradation to control and alter cell function, Curr. Opin. Biotechnol., 36, 199, 10.1016/j.copbio.2015.08.023
Yu, 2018, Autophagy pathway: cellular and molecular mechanisms, Autophagy, 14, 207, 10.1080/15548627.2017.1378838
Zhang, 2017, Optogenetic approaches to drug discovery in neuroscience and beyond, Trends Biotechnol., 35, 625, 10.1016/j.tibtech.2017.04.002
Zhang, 2003, Determinants of proteasome recognition of ornithine decarboxylase, a ubiquitin-independent substrate, EMBO J., 22, 1488, 10.1093/emboj/cdg158
Zhang, 2003, Exploring the functional complexity of cellular proteins by protein knockout, Proc. Natl. Acad. Sci., 100, 14127, 10.1073/pnas.2233012100
Zhang, 2004, Proteasomes begin ornithine decarboxylase digestion at the C terminus, J. Biol. Chem., 279, 20959, 10.1074/jbc.M314043200
Zhao, 2018, Quantitatively predictable control of cellular protein levels through proteasomal degradation, ACS Synth. Biol., 7, 540, 10.1021/acssynbio.7b00325
Zheng, 2000, Structure of a c-Cbl-UbcH7 complex: RING domain function in ubiquitin-protein ligases, Cell, 102, 533, 10.1016/S0092-8674(00)00057-X
Zhou, 2000, Harnessing the ubiquitination machinery to target the degradation of specific cellular proteins, Mol. Cell, 6, 751, 10.1016/S1097-2765(00)00074-5