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Xie H, Liang JJ, Wang YL, Hu TX, Wang JY, Yang RH, Yan JK, Zhang QR, Xu X, Liu HM, Ke Y. The design, synthesis and anti-tumor mechanism study of new androgen receptor degrader. Eur J Med Chem 2020; 204:112512. [PMID: 32736229 DOI: 10.1016/j.ejmech.2020.112512] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 05/20/2020] [Accepted: 05/24/2020] [Indexed: 12/15/2022]
Abstract
Targeted protein degradation using small molecules is a novel strategy for drug development. In order to solve the problem of drug resistance in the treatment of prostate cancer, proteolysis-targeting chimeras (PROTAC) was introduced into the design of anti-prostate cancer derivatives. In this work, we synthesized two series of selective androgen receptor degraders (SARDs) containing the hydrophobic degrons with different linker, and then investigated the structure-activity relationships of these hybrid compounds. Most of the synthesized compounds exhibited moderate to good activity against all the cancer cell lines selected. Among them, compound A9 displayed potent inhibitory activity against LNCaP prostate cancer cell line with IC50 values of 1.75 μM, as well as excellent AR degradation activity. Primary mechanism studies elucidated compound A9 arrested cell cycle at G0/G1 phase and induced a mild apoptotic response in LNCaP cells. Further study indicated that the degradation of AR was mediated through proteasome-mediated process. For all these reasons, compound A9 held promising potential as anti-proliferative agent for the development of highly efficient SARDs for drug-resistance prostate cancer therapies.
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Affiliation(s)
- Hang Xie
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, PR China; Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Zhengzhou 450001, PR China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, PR China
| | - Jian-Jia Liang
- School of Pharmacy, Wuhan University, Wuhan, Hubei, 430072, PR China.
| | - Ya-Lei Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, PR China; Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Zhengzhou 450001, PR China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, PR China
| | - Tian-Xing Hu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, PR China; Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Zhengzhou 450001, PR China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, PR China
| | - Jin-Yi Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, PR China; Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Zhengzhou 450001, PR China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, PR China
| | - Rui-Hua Yang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, PR China; Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Zhengzhou 450001, PR China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, PR China
| | - Jun-Ke Yan
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, PR China; Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Zhengzhou 450001, PR China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, PR China
| | - Qiu-Rong Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, PR China; Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Zhengzhou 450001, PR China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, PR China
| | - Xia Xu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, PR China; Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Zhengzhou 450001, PR China.
| | - Hong-Min Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, PR China; Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Zhengzhou 450001, PR China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, PR China.
| | - Yu Ke
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, PR China; Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Zhengzhou 450001, PR China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, PR China.
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2
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Chen W, Werdann M, Zhang Y. The auxin-inducible degradation system enables conditional PERIOD protein depletion in the nervous system of Drosophila melanogaster. FEBS J 2018; 285:4378-4393. [PMID: 30321477 DOI: 10.1111/febs.14677] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/26/2018] [Accepted: 10/11/2018] [Indexed: 01/07/2023]
Abstract
Tools that allow inducible and reversible depletion of target proteins are critical for biological studies. The plant-derived auxin-inducible degradation system (AID) enables the degradation of target proteins tagged with the AID motif. This system has been recently employed in mammalian cells as well as in Caenorhabditis elegans and Drosophila. To test the utility of the AID approach in the nervous system, we used circadian locomotor rhythms as a model and applied the AID method to temporally and spatially degrade PERIOD (PER), a critical pacemaker protein in Drosophila. We found that the period locus can be efficiently tagged with the AID motif by CRISPR/Cas9-based genome editing without disrupting PER function. Moreover, we demonstrated that the AID system could be used to induce rapid and efficient protein degradation in the nervous system as shown by effects on circadian and sleep behaviors. Furthermore, the protein degradation by AID was rapidly reversible after auxin removal. Together, our results show that the AID system provides a powerful tool for behavior studies in Drosophila.
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Affiliation(s)
- Wenfeng Chen
- Institute of Life Sciences, Fuzhou University, Fuzhou, China.,Department of Biology, University of Nevada Reno, NV, USA
| | | | - Yong Zhang
- Department of Biology, University of Nevada Reno, NV, USA
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3
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Samejima K, Booth DG, Ogawa H, Paulson JR, Xie L, Watson CA, Platani M, Kanemaki MT, Earnshaw WC. Functional analysis after rapid degradation of condensins and 3D-EM reveals chromatin volume is uncoupled from chromosome architecture in mitosis. J Cell Sci 2018; 131:jcs.210187. [PMID: 29361541 PMCID: PMC5868952 DOI: 10.1242/jcs.210187] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 01/15/2018] [Indexed: 01/01/2023] Open
Abstract
The requirement for condensin in chromosome formation in somatic cells remains unclear, as imperfectly condensed chromosomes do form in cells depleted of condensin by conventional methodologies. In order to dissect the roles of condensin at different stages of vertebrate mitosis, we have established a versatile cellular system that combines auxin-mediated rapid degradation with chemical genetics to obtain near-synchronous mitotic entry of chicken DT40 cells in the presence and absence of condensin. We analyzed the outcome by live- and fixed-cell microscopy methods, including serial block face scanning electron microscopy with digital reconstruction. Following rapid depletion of condensin, chromosomal defects were much more obvious than those seen after a slow depletion of condensin. The total mitotic chromatin volume was similar to that in control cells, but a single mass of mitotic chromosomes was clustered at one side of a bent mitotic spindle. Cultures arrest at prometaphase, eventually exiting mitosis without segregating chromosomes. Experiments where the auxin concentration was titrated showed that different condensin levels are required for anaphase chromosome segregation and formation of a normal chromosome architecture. This article has an associated First Person interview with the first author of the paper. Summary: Rapid condensin depletion reveals that different condensin levels are required for mitotic chromosome architecture and segregation. Condensin is not required for chromatin volume compaction during mitosis.
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Affiliation(s)
- Kumiko Samejima
- Wellcome Centre for Cell Biology, University of Edinburgh, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
| | - Daniel G Booth
- Wellcome Centre for Cell Biology, University of Edinburgh, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
| | - Hiromi Ogawa
- Wellcome Centre for Cell Biology, University of Edinburgh, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
| | - James R Paulson
- Department of Chemistry, University of Wisconsin-Oshkosh, 800 Algoma Blvd, Oshkosh, WI 54901, USA
| | - Linfeng Xie
- Department of Chemistry, University of Wisconsin-Oshkosh, 800 Algoma Blvd, Oshkosh, WI 54901, USA
| | - Cara A Watson
- Wellcome Centre for Cell Biology, University of Edinburgh, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
| | - Melpomeni Platani
- Wellcome Centre for Cell Biology, University of Edinburgh, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
| | - Masato T Kanemaki
- Division of Molecular Cell Engineering, National Institute of Genetics, ROIS, and Department of Genetics, SOKENDAI, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - William C Earnshaw
- Wellcome Centre for Cell Biology, University of Edinburgh, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
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4
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Lv X, Wang F, Zhou P, Ye L, Xie W, Xu H, Yu H. Dual regulation of cytoplasmic and mitochondrial acetyl-CoA utilization for improved isoprene production in Saccharomyces cerevisiae. Nat Commun 2016; 7:12851. [PMID: 27650330 PMCID: PMC5036000 DOI: 10.1038/ncomms12851] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 08/08/2016] [Indexed: 12/18/2022] Open
Abstract
Microbial production of isoprene from renewable feedstock is a promising alternative to traditional petroleum-based processes. Currently, efforts to improve isoprenoid production in Saccharomyces cerevisiae mainly focus on cytoplasmic engineering, whereas comprehensive engineering of multiple subcellular compartments is rarely reported. Here, we propose dual metabolic engineering of cytoplasmic and mitochondrial acetyl-CoA utilization to boost isoprene synthesis in S. cerevisiae. This strategy increases isoprene production by 2.1-fold and 1.6-fold relative to the recombinant strains with solely mitochondrial or cytoplasmic engineering, respectively. By combining a modified reiterative recombination system for rapid pathway assembly, a two-phase culture process for dynamic metabolic regulation, and aerobic fed-batch fermentation for sufficient supply of acetyl-coA and carbon, we achieve 2527, mg l(-1) of isoprene, which is the highest ever reported in engineered eukaryotes. We propose this strategy as an efficient approach to enhancing isoprene production in yeast, which might open new possibilities for bioproduction of other value-added chemicals.
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Affiliation(s)
- Xiaomei Lv
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Fan Wang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Pingping Zhou
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Lidan Ye
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China.,Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Zhejiang University, Hangzhou 310027, China
| | - Wenping Xie
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Haoming Xu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Hongwei Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
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5
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Trost M, Blattner AC, Lehner CF. Regulated protein depletion by the auxin-inducible degradation system in Drosophila melanogaster. Fly (Austin) 2016; 10:35-46. [PMID: 27010248 DOI: 10.1080/19336934.2016.1168552] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The analysis of consequences resulting after experimental elimination of gene function has been and will continue to be an extremely successful strategy in biological research. Mutational elimination of gene function has been widely used in the fly Drosophila melanogaster. RNA interference is used extensively as well. In the fly, exceptionally precise temporal and spatial control over elimination of gene function can be achieved in combination with sophisticated transgenic approaches and clonal analyses. However, the methods that act at the gene and transcript level cannot eliminate protein products which are already present at the time when mutant cells are generated or RNA interference is started. Targeted inducible protein degradation is therefore of considerable interest for controlled rapid elimination of gene function. To this end, a degradation system was developed in yeast exploiting TIR1, a plant F box protein, which can recruit proteins with an auxin-inducible degron to an E3 ubiquitin ligase complex, but only in the presence of the phytohormone auxin. Here we demonstrate that the auxin-inducible degradation system functions efficiently also in Drosophila melanogaster. Neither auxin nor TIR1 expression have obvious toxic effects in this organism, and in combination they result in rapid degradation of a target protein fused to the auxin-inducible degron.
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Affiliation(s)
- Martina Trost
- a Institute of Molecular Life Sciences (IMLS), University of Zurich , Zurich , Switzerland
| | - Ariane C Blattner
- a Institute of Molecular Life Sciences (IMLS), University of Zurich , Zurich , Switzerland
| | - Christian F Lehner
- a Institute of Molecular Life Sciences (IMLS), University of Zurich , Zurich , Switzerland
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6
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Natsume T, Kiyomitsu T, Saga Y, Kanemaki MT. Rapid Protein Depletion in Human Cells by Auxin-Inducible Degron Tagging with Short Homology Donors. Cell Rep 2016; 15:210-218. [PMID: 27052166 DOI: 10.1016/j.celrep.2016.03.001] [Citation(s) in RCA: 389] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/28/2016] [Accepted: 02/24/2016] [Indexed: 01/31/2023] Open
Abstract
Studying the role of essential proteins is dependent upon a method for rapid inactivation, in order to study the immediate phenotypic consequences. Auxin-inducible degron (AID) technology allows rapid depletion of proteins in animal cells and fungi, but its application to human cells has been limited by the difficulties of tagging endogenous proteins. We have developed a simple and scalable CRISPR/Cas-based method to tag endogenous proteins in human HCT116 and mouse embryonic stem (ES) cells by using donor constructs that harbor synthetic short homology arms. Using a combination of AID tagging with CRISPR/Cas, we have generated conditional alleles of essential nuclear and cytoplasmic proteins in HCT116 cells, which can then be depleted very rapidly after the addition of auxin to the culture medium. This approach should greatly facilitate the functional analysis of essential proteins, particularly those of previously unknown function.
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Affiliation(s)
- Toyoaki Natsume
- Center of Frontier Research, National Institute of Genetics, Research Organization of Information and Systems, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Tomomi Kiyomitsu
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan; PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Yumiko Saga
- Division of Mammalian Development, Genetic Strains Research Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, SOKENDAI, Yata 1111, Mishima, Shizuoka 411-8540, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masato T Kanemaki
- Center of Frontier Research, National Institute of Genetics, Research Organization of Information and Systems, Yata 1111, Mishima, Shizuoka 411-8540, Japan; PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan; Department of Genetics, SOKENDAI, Yata 1111, Mishima, Shizuoka 411-8540, Japan.
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7
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Proteolysis targeting peptide (PROTAP) strategy for protein ubiquitination and degradation. Biochem Biophys Res Commun 2016; 470:936-40. [DOI: 10.1016/j.bbrc.2016.01.158] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 01/25/2016] [Indexed: 11/21/2022]
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8
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Selectable one-step PCR-mediated integration of a degron for rapid depletion of endogenous human proteins. Biotechniques 2016; 60:69-74. [PMID: 26842351 DOI: 10.2144/000114378] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 11/11/2015] [Indexed: 01/13/2023] Open
Abstract
Manipulation of protein stability with ligand-regulated degron fusions is a powerful method for investigating gene function. We developed a selectable cassette for easy C-terminal tagging of endogenous human proteins with the E. coli dihydrofolate reductase (eDHFR) degron using CRISPR/Cas9 genome editing. This cassette permits high-efficiency recovery of correct integration events using an in-frame self-cleaving 2A peptide and the puromycin resistance gene. PCR amplified donor eDHFR cassette fragments with 100 bases of homology on each end are integrated by homology-directed repair (HDR) of guide RNA (gRNA)-targeted double-stranded DNA breaks at the 3' ends of open reading frames (ORFs). As proof of principle, we generated cell lines in which three endogenous proteins were tagged with the eDHFR degron. When the antibiotic trimethoprim is removed from the media, each of the eDHFR-tagged proteins was depleted by >90% within 2-4 h, and this depletion was reversed by re-addition of trimethoprim. Since puromycin selection permits recovery of in-frame degron fusions with high efficiency using only 100-bp long regions of homology, this method should be applicable on a genome-wide scale for generating libraries of conditional mutant cell lines.
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9
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Auffenberg E, Jurik A, Mattusch C, Stoffel R, Genewsky A, Namendorf C, Schmid RM, Rammes G, Biel M, Uhr M, Moosmang S, Michalakis S, Wotjak CT, Thoeringer CK. Remote and reversible inhibition of neurons and circuits by small molecule induced potassium channel stabilization. Sci Rep 2016; 6:19293. [PMID: 26757616 PMCID: PMC4725838 DOI: 10.1038/srep19293] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 12/09/2015] [Indexed: 01/12/2023] Open
Abstract
Manipulating the function of neurons and circuits that translate electrical and chemical signals into behavior represents a major challenges in neuroscience. In addition to optogenetic methods using light-activatable channels, pharmacogenetic methods with ligand induced modulation of cell signaling and excitability have been developed. However, they are largely based on ectopic expression of exogenous or chimera proteins. Now, we describe the remote and reversible expression of a Kir2.1 type potassium channel using the chemogenetic technique of small molecule induced protein stabilization. Based on shield1-mediated shedding of a destabilizing domain fused to a protein of interest and inhibition of protein degradation, this principle has been adopted for biomedicine, but not in neuroscience so far. Here, we apply this chemogenetic approach in brain research for the first time in order to control a potassium channel in a remote and reversible manner. We could show that shield1-mediated ectopic Kir2.1 stabilization induces neuronal silencing in vitro and in vivo in the mouse brain. We also validated this novel pharmacogenetic method in different neurobehavioral paradigms.The DD-Kir2.1 may complement the existing portfolio of pharmaco- and optogenetic techniques for specific neuron manipulation, but it may also provide an example for future applications of this principle in neuroscience research.
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Affiliation(s)
- Eva Auffenberg
- Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Germany
| | - Angela Jurik
- Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Germany
| | - Corinna Mattusch
- Institute of Anesthesiology, Technical University of Munich, Germany
| | - Rainer Stoffel
- Max Planck Institute of Psychiatry, Department of Stress Physiology and Neurogenetics, Munich, Germany
| | - Andreas Genewsky
- Max Planck Institute of Psychiatry, Department of Stress Physiology and Neurogenetics, Munich, Germany
| | - Christian Namendorf
- Max Planck Institute of Psychiatry, Department of Stress Physiology and Neurogenetics, Munich, Germany
| | - Roland M Schmid
- Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Germany
| | - Gerhard Rammes
- Institute of Anesthesiology, Technical University of Munich, Germany
| | - Martin Biel
- Center for Integrated Protein Science Munich (CIPSM) and Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-University of Munich, Germany
| | - Manfred Uhr
- Max Planck Institute of Psychiatry, Department of Stress Physiology and Neurogenetics, Munich, Germany
| | - Sven Moosmang
- Institute of Pharmacology, Technical University of Munich, Germany
| | - Stylianos Michalakis
- Center for Integrated Protein Science Munich (CIPSM) and Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-University of Munich, Germany
| | - Carsten T Wotjak
- Max Planck Institute of Psychiatry, Department of Stress Physiology and Neurogenetics, Munich, Germany
| | - Christoph K Thoeringer
- Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Germany
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10
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Abstract
Regulation of protein stability is a fundamental process in eukaryotic cells and pivotal to, e.g., cell cycle progression, faithful chromosome segregation, or protein quality control. Synthetic regulation of protein stability requires conditional degradation sequences (degrons) that induce a stability switch upon a specific signal. Fusion to a selected target protein permits to influence virtually every process in a cell. Light as signal is advantageous due to its precise applicability in time, space, quality, and quantity. Light control of protein stability was achieved by fusing the LOV2 photoreceptor domain of Arabidopsis thaliana phototropin1 with a synthetic degron (cODC1) derived from the carboxy-terminal degron of ornithine decarboxylase to obtain the photosensitive degron (psd) module. The psd module can be attached to the carboxy terminus of target proteins that are localized to the cytosol or nucleus to obtain light control over their stability. Blue light induces structural changes in the LOV2 domain, which in turn lead to activation of the degron and thus proteasomal degradation of the whole fusion protein. Variants of the psd module with diverse characteristics are useful to fine-tune the stability of a selected target at permissive (darkness) and restrictive conditions (blue light).
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11
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Devrekanli A, Kanemaki MT. Conditional Budding Yeast Mutants with Temperature-Sensitive and Auxin-Inducible Degrons for Screening of Suppressor Genes. Methods Mol Biol 2015; 1369:257-78. [PMID: 26519318 DOI: 10.1007/978-1-4939-3145-3_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The conditional control of protein expression is useful to characterize the function of proteins, especially of those that are essential for cell viability. Two degron-based systems, temperature-sensitive and auxin-inducible degrons, can be used to generate conditional mutants of budding yeast, simply by transforming appropriate cells with PCR-amplified DNA. We describe a protocol for the generation of temperature-sensitive and auxin-inducible degron mutants. We also show that a conditional mutant with few spontaneous revertants was generated by combining two degron systems for the Inn1 protein. Finally, we describe a suppressor screening method that uses the dual degron-Inn1 mutant to identify mutant proteins that suppress Inn1-K31A, which has a defect in cytokinesis.
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Affiliation(s)
- Asli Devrekanli
- Department of Molecular Biology and Genetics, Canik Basari University, Gürgenyatak Köyü, Samsun, 55080, Turkey.
| | - Masato T Kanemaki
- Center of Frontier Research, National Institute of Genetics, Research Organization of Information and Systems, SOKENDAI, Yata 1111, Mishima, Shizuoka, 411-8540, Japan. .,Department of Genetics, SOKENDAI, Mishima, Shizuoka, Japan. .,JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
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12
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Nishimura K, Kanemaki MT. Rapid Depletion of Budding Yeast Proteins via the Fusion of an Auxin-Inducible Degron (AID). ACTA ACUST UNITED AC 2014; 64:20.9.1-16. [PMID: 25181302 DOI: 10.1002/0471143030.cb2009s64] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The auxin-inducible degron (AID) system allows the rapid and reversible proteolysis of proteins of interest, and enables the generation of conditional mutants of budding yeast. The construction of budding yeast AID mutants is simple, and the effect of depletion of essential proteins on proliferation can be confirmed by analyzing their phenotype. In this protocol, we describe a procedure to generate AID mutants of budding yeast via a simple transformation using PCR-amplified DNA. We also describe methods to confirm the depletion of proteins of interest that are required for proliferation by serial-dilution and liquid-culture assays.
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Affiliation(s)
- Kohei Nishimura
- Center of Frontier Research, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka, Japan
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13
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Leśniewska K, Warbrick E, Ohkura H. Peptide aptamers define distinct EB1- and EB3-binding motifs and interfere with microtubule dynamics. Mol Biol Cell 2014; 25:1025-36. [PMID: 24478452 PMCID: PMC3967968 DOI: 10.1091/mbc.e13-08-0504] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
This study isolated many peptide aptamers containing the SxIP motif that binds to Drosophila EB1 and human EB1 and EB3. Interaction sequences are similar to but distinct from each other. Aptamers can competitively displace endogenous EB1-interacting proteins from microtubule plus ends, and their expression in developing flies alters microtubule dynamics. EB1 is a conserved protein that plays a central role in regulating microtubule dynamics and organization. It binds directly to microtubule plus ends and recruits other plus end–localizing proteins. Most EB1-binding proteins contain a Ser–any residue–Ile-Pro (SxIP) motif. Here we describe the isolation of peptide aptamers with optimized versions of this motif by screening for interaction with the Drosophila EB1 protein. The use of small peptide aptamers to competitively inhibit protein interaction and function is becoming increasingly recognized as a powerful technique. We show that SxIP aptamers can bind microtubule plus ends in cells and functionally act to displace interacting proteins by competitive binding. Their expression in developing flies can interfere with microtubules, altering their dynamics. We also identify aptamers binding to human EB1 and EB3, which have sequence requirements similar to but distinct from each other and from Drosophila EB1. This suggests that EB1 paralogues within one species may interact with overlapping but distinct sets of proteins in cells.
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Affiliation(s)
- Karolina Leśniewska
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom Division of Molecular Medicine, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
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