1
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Verbič A, Lebar T, Praznik A, Jerala R. Subunits of an E3 Ligase Complex as Degrons for Efficient Degradation of Cytosolic, Nuclear, and Membrane Proteins. ACS Synth Biol 2024; 13:792-803. [PMID: 38404221 PMCID: PMC10949250 DOI: 10.1021/acssynbio.3c00588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/27/2024]
Abstract
Protein degradation is a highly regulated cellular process crucial to enable the high dynamic range of the response to external and internal stimuli and to balance protein biosynthesis to maintain cell homeostasis. Within mammalian cells, hundreds of E3 ubiquitin ligases target specific protein substrates and could be repurposed for synthetic biology. Here, we present a systematic analysis of the four protein subunits of the multiprotein E3 ligase complex as scaffolds for the designed degrons. While all of them were functional, the fusion of a fragment of Skp1 with the target protein enabled the most effective degradation. Combination with heterodimerizing peptides, protease substrate sites, and chemically inducible dimerizers enabled the regulation of protein degradation. While the investigated subunits of E3 ligases showed variable degradation efficiency of the membrane and cytosolic and nuclear proteins, the bipartite SSD (SOCSbox-Skp1(ΔC111)) degron enabled fast degradation of protein targets in all tested cellular compartments, including the nucleus and plasma membrane, in different cell lines and could be chemically regulated. These subunits could be employed for research as well as for diverse applications, as demonstrated in the regulation of Cas9 and chimeric antigen receptor proteins.
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Affiliation(s)
- Anže Verbič
- Department of Synthetic Biology
and Immunology, National Institute of Chemistry, Ljubljana 1000, Slovenia
| | | | - Arne Praznik
- Department of Synthetic Biology
and Immunology, National Institute of Chemistry, Ljubljana 1000, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology
and Immunology, National Institute of Chemistry, Ljubljana 1000, Slovenia
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2
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Song J, Fan J, Fan C, He N, Ye X, Cao M, Yuan J. A Layered Genetic Design Enables the Yeast Galactose Regulon to Respond to Cyanamide. ACS Synth Biol 2023; 12:2783-2788. [PMID: 37603344 DOI: 10.1021/acssynbio.3c00241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
The commonly used expression systems in Saccharomyces cerevisiae typically rely on either constitutive or galactose-regulated promoters. The lack of inducible systems in S. cerevisiae limits the precise temporal regulation of protein function and yeast metabolism. We herein repurposed the galactose-regulated system to make it respond to cyanamide. By using a cyanamide-inducible DDI2 promoter to control Gal4 expression in CEN.PK2-1C with Δgal80, a tight and graded cyanamide-inducible GAL system with an enhanced signal output was constructed. Subsequently, we demonstrated that the cyanamide-inducible GAL system was capable of tightly regulating the pentafunctional Aro1 protein to achieve conditional shikimate pathway activity. Taken together, the cyanamide-inducible GAL system could be implemented for both fundamental research and applied biotechnology.
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Affiliation(s)
- Jingya Song
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian 361102, China
| | - Jian Fan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian 361102, China
| | - Cong Fan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian 361102, China
| | - Nike He
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian 361102, China
| | - Xixi Ye
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian 361102, China
| | - Mingfeng Cao
- College of Chemistry and Chemical Engineering, Xiamen University, Fujian 361005, China
| | - Jifeng Yuan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian 361102, China
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3
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Zhou J, Ge Q, Wang D, Guo Q, Tao Y. Engineering a modular double-transmembrane synthetic receptor system for customizing cellular programs. Cell Rep 2023; 42:112385. [PMID: 37043348 DOI: 10.1016/j.celrep.2023.112385] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 02/21/2023] [Accepted: 03/28/2023] [Indexed: 04/13/2023] Open
Abstract
Implementation of designer receptors in engineered cells confers them to sense a particular physiological or disease state and respond with user-defined programs. To expand the therapeutic application scope of engineered cells, synthetic receptors realized through different strategies are in great demand. Here, we develop a synthetic receptor system that exerts dual control by incorporating two transmembrane helices for the signal chain. Together with a sensor-actuator device with minimal background signals and a positive loop circuit, this receptor system can sensitively respond to extracellular protein signals. We demonstrate that this synthetic receptor system can be readily adapted to respond to various inputs, such as interleukin-1 (IL-1), programmed death ligand 1 (PD-L1), and HER2, and release customized outputs, including fluorescence signals and the therapeutic molecule IL-2. The robust signaling ability and generality of this receptor system promise it to be a useful tool in the field of cell engineering for fundamental research and translational applications.
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Affiliation(s)
- Jingru Zhou
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, P.R. China
| | - Qiangqiang Ge
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, P.R. China
| | - Dandan Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, P.R. China
| | - Qiong Guo
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, P.R. China.
| | - Yuyong Tao
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, P.R. China.
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4
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Chernov KG, Manoilov KY, Oliinyk OS, Shcherbakova DM, Verkhusha VV. Photodegradable by Yellow-Orange Light degFusionRed Optogenetic Module with Autocatalytically Formed Chromophore. Int J Mol Sci 2023; 24:6526. [PMID: 37047499 PMCID: PMC10095432 DOI: 10.3390/ijms24076526] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/26/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
Optogenetic systems driven by yellow-orange light are required for the simultaneous regulation of several cellular processes. We have engineered the red fluorescent protein FusionRed into a 26 kDa monomeric optogenetic module, called degFusionRed. Unlike other fluorescent protein-based optogenetic domains, which exhibit light-induced self-inactivation by generating reactive oxygen species, degFusionRed undergoes proteasomal degradation upon illumination with 567 nm light. Similarly to the parent protein, degFusionRed has minimal absorbance at 450 nm and above 650 nm, making it spectrally compatible with blue and near-infrared-light-controlled optogenetic tools. The autocatalytically formed chromophore provides degFusionRed with an additional advantage over most optogenetic tools that require the binding of the exogenous chromophores, the amount of which varies in different cells. The degFusionRed efficiently performed in the engineered light-controlled transcription factor and in the targeted photodegradation of the protein of interest, demonstrating its versatility as the optogenetic module of choice for spectral multiplexed interrogation of various cellular processes.
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Affiliation(s)
| | - Kyrylo Yu. Manoilov
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Olena S. Oliinyk
- Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Daria M. Shcherbakova
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Vladislav V. Verkhusha
- Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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5
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Winckler LI, Dissmeyer N. TEV protease cleavage in generation of artificial substrate proteins bearing neo-N-termini. Methods Enzymol 2023. [PMID: 37532397 DOI: 10.1016/bs.mie.2023.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
Abstract
The tobacco etch virus (TEV) protease is widely used in in vitro and in vivo approaches for the removal of affinity tags from fusion proteins or the generation of proteins with a desired N-terminal amino acid. Processing of fusion proteins by the TEV protease can either be achieved by encoding the TEV protease and its recognition site on one construct (self-cleavage) or on two different constructs (co-expression). Here, we compare the efficiency of the self-splitting approach to the co-expression approach.
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6
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Milholland KL, AbdelKhalek A, Baker KM, Hoda S, DeMarco AG, Naughton NH, Koeberlein AN, Lorenz GR, Anandasothy K, Esperilla-Muñoz A, Narayanan SK, Correa-Bordes J, Briggs SD, Hall MC. Cdc14 phosphatase contributes to cell wall integrity and pathogenesis in Candida albicans. Front Microbiol 2023; 14:1129155. [PMID: 36876065 PMCID: PMC9977832 DOI: 10.3389/fmicb.2023.1129155] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 01/26/2023] [Indexed: 02/18/2023] Open
Abstract
The Cdc14 phosphatase family is highly conserved in fungi. In Saccharomyces cerevisiae, Cdc14 is essential for down-regulation of cyclin-dependent kinase activity at mitotic exit. However, this essential function is not broadly conserved and requires only a small fraction of normal Cdc14 activity. Here, we identified an invariant motif in the disordered C-terminal tail of fungal Cdc14 enzymes that is required for full enzyme activity. Mutation of this motif reduced Cdc14 catalytic rate and provided a tool for studying the biological significance of high Cdc14 activity. A S. cerevisiae strain expressing the reduced-activity hypomorphic mutant allele (cdc14hm ) as the sole source of Cdc14 proliferated like the wild-type parent strain but exhibited an unexpected sensitivity to cell wall stresses, including chitin-binding compounds and echinocandin antifungal drugs. Sensitivity to echinocandins was also observed in Schizosaccharomyces pombe and Candida albicans strains lacking CDC14, suggesting this phenotype reflects a novel and conserved function of Cdc14 orthologs in mediating fungal cell wall integrity. In C. albicans, the orthologous cdc14hm allele was sufficient to elicit echinocandin hypersensitivity and perturb cell wall integrity signaling. It also caused striking abnormalities in septum structure and the same cell separation and hyphal differentiation defects previously observed with cdc14 gene deletions. Since hyphal differentiation is important for C. albicans pathogenesis, we assessed the effect of reduced Cdc14 activity on virulence in Galleria mellonella and mouse models of invasive candidiasis. Partial reduction in Cdc14 activity via cdc14hm mutation severely impaired C. albicans virulence in both assays. Our results reveal that high Cdc14 activity is important for C. albicans cell wall integrity and pathogenesis and suggest that Cdc14 may be worth future exploration as an antifungal drug target.
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Affiliation(s)
- Kedric L Milholland
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Ahmed AbdelKhalek
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, United States
| | - Kortany M Baker
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Smriti Hoda
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Andrew G DeMarco
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Noelle H Naughton
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Angela N Koeberlein
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Gabrielle R Lorenz
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Kartikan Anandasothy
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | | | - Sanjeev K Narayanan
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, United States
| | - Jaime Correa-Bordes
- Department of Biomedical Sciences, Universidad de Extremadura, Badajoz, Spain
| | - Scott D Briggs
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States.,Institute for Cancer Research, Purdue University, West Lafayette, IN, United States
| | - Mark C Hall
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States.,Institute for Cancer Research, Purdue University, West Lafayette, IN, United States
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7
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Zhang T, Liu C, Li W, Kuang J, Qiu XY, Min L, Zhu L. Targeted protein degradation in mammalian cells: A Promising Avenue toward Future. Comput Struct Biotechnol J 2022; 20:5477-5489. [PMID: 36249565 PMCID: PMC9535385 DOI: 10.1016/j.csbj.2022.09.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/24/2022] [Accepted: 09/26/2022] [Indexed: 12/04/2022] Open
Abstract
In the eukaryotic cellular milieu, proteins are continuously synthesized and degraded effectively via endogenous protein degradation machineries such as the ubiquitin–proteasome and lysosome pathways. By reengineering and repurposing these natural protein regulatory mechanisms, the targeted protein degradation (TPD) strategies are presenting biologists with powerful tools to manipulate the abundance of proteins of interest directly, precisely, and reversibly at the post-translational level. In recent years, TPD is gaining massive attention and is recognized as a paradigm shift both in basic research, application-oriented synthetic biology, and pioneering clinical work. In this review, we summarize the updated information, especially the engineering efforts and developmental route, of current state-of-the-art TPD technology such as Trim-Away, LYTACs, and AUTACs. Besides, the general design principle, benefits, problems, and opportunities to be addressed were further analyzed, with the aim of providing guidelines for exploration, discovery, and further application of novel TPD tools in the future.
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8
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Mahrou B, Pirhanov A, Alijanvand MH, Cho YK, Shin YJ. Degradation-driven protein level oscillation in the yeast Saccharomyces cerevisiae. Biosystems 2022; 219:104717. [PMID: 35690291 DOI: 10.1016/j.biosystems.2022.104717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 06/03/2022] [Accepted: 06/03/2022] [Indexed: 11/02/2022]
Abstract
Generating robust, predictable perturbations in cellular protein levels will advance our understanding of protein function and enable the control of physiological outcomes in biotechnology applications. Timed periodic changes in protein levels play a critical role in the cell division cycle, cellular stress response, and development. Here we report the generation of robust protein level oscillations by controlling the protein degradation rate in the yeast Saccharomyces cerevisiae. Using a photo-sensitive degron and red fluorescent proteins as reporters, we show that under constitutive transcriptional induction, repeated triangular protein level oscillations as fast as 5-10 min-scale can be generated by modulating the protein degradation rate. Consistent with oscillations generated though transcriptional control, we observed a continuous decrease in the magnitude of oscillations as the input modulation frequency increased, indicating low-pass filtering of input perturbation. By using two red fluorescent proteins with distinct maturation times, we show that the oscillations in protein level is largely unaffected by delays originating from functional protein formation. Our study demonstrates the potential for repeated control of protein levels by controlling the protein degradation rate without altering the transcription rate.
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Affiliation(s)
- Bahareh Mahrou
- Biomedical Engineering Department, University of Connecticut, Storrs, CT, 06269, USA; Electrical Engineering Department, University of Connecticut, Storrs, CT, 06069, USA.
| | - Azady Pirhanov
- Biomedical Engineering Department, University of Connecticut, Storrs, CT, 06269, USA
| | - Moluk Hadi Alijanvand
- Department of Epidemiology and Biostatistics, School of Health, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Yong Ku Cho
- Biomedical Engineering Department, University of Connecticut, Storrs, CT, 06269, USA; Chemical and Biomolecular Engineering Department, University of Connecticut, Storrs, CT, 06269, USA.
| | - Yong-Jun Shin
- Biomedical Engineering Department, University of Connecticut, Storrs, CT, 06269, USA
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9
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Jadhav P, Chen Y, Butzin N, Buceta J, Urchueguía A. Bacterial degrons in synthetic circuits. Open Biol 2022; 12:220180. [PMID: 35975648 PMCID: PMC9382460 DOI: 10.1098/rsob.220180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial proteases are a promising post-translational regulation strategy in synthetic circuits because they recognize specific amino acid degradation tags (degrons) that can be fine-tuned to modulate the degradation levels of tagged proteins. For this reason, recent efforts have been made in the search for new degrons. Here we review the up-to-date applications of degradation tags for circuit engineering in bacteria. In particular, we pay special attention to the effects of degradation bottlenecks in synthetic oscillators and introduce mathematical approaches to study queueing that enable the quantitative modelling of proteolytic queues.
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Affiliation(s)
- Prajakta Jadhav
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Yanyan Chen
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicholas Butzin
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Javier Buceta
- Institute for Integrative Systems Biology (I2SysBio, CSIC-UV), Paterna, Valencia 46980, Spain
| | - Arantxa Urchueguía
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA.,Institute for Integrative Systems Biology (I2SysBio, CSIC-UV), Paterna, Valencia 46980, Spain
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10
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Pfeiffer ML, Winkler J, Van Damme D, Jacobs TB, Nowack MK. Conditional and tissue-specific approaches to dissect essential mechanisms in plant development. CURRENT OPINION IN PLANT BIOLOGY 2022; 65:102119. [PMID: 34653951 PMCID: PMC7612331 DOI: 10.1016/j.pbi.2021.102119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 05/19/2023]
Abstract
Reverse genetics approaches are routinely used to investigate gene function. However, mutations, especially in critical genes, can lead to pleiotropic effects as severe as lethality, thus limiting functional studies in specific contexts. Approaches that allow for modifications of genes or gene products in a specific spatial or temporal setting can overcome these limitations. The advent of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) technologies has not only revolutionized targeted genome modification in plants but also enabled new possibilities for inducible and tissue-specific manipulation of gene functions at the DNA and RNA levels. In addition, novel approaches for the direct manipulation of target proteins have been introduced in plant systems. Here, we review the current development in tissue-specific and conditional manipulation approaches at the DNA, RNA, and protein levels.
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Affiliation(s)
- Marie L Pfeiffer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Joanna Winkler
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Thomas B Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, 9052, Ghent, Belgium.
| | - Moritz K Nowack
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, 9052, Ghent, Belgium.
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11
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Nakanishi H. Protein-Based Systems for Translational Regulation of Synthetic mRNAs in Mammalian Cells. Life (Basel) 2021; 11:life11111192. [PMID: 34833067 PMCID: PMC8621430 DOI: 10.3390/life11111192] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/31/2021] [Accepted: 11/01/2021] [Indexed: 11/16/2022] Open
Abstract
Synthetic mRNAs, which are produced by in vitro transcription, have been recently attracting attention because they can express any transgenes without the risk of insertional mutagenesis. Although current synthetic mRNA medicine is not designed for spatiotemporal or cell-selective regulation, many preclinical studies have developed the systems for the translational regulation of synthetic mRNAs. Such translational regulation systems will cope with high efficacy and low adverse effects by producing the appropriate amount of therapeutic proteins, depending on the context. Protein-based regulation is one of the most promising approaches for the translational regulation of synthetic mRNAs. As synthetic mRNAs can encode not only output proteins but also regulator proteins, all components of protein-based regulation systems can be delivered as synthetic mRNAs. In addition, in the protein-based regulation systems, the output protein can be utilized as the input for the subsequent regulation to construct multi-layered gene circuits, which enable complex and sophisticated regulation. In this review, I introduce what types of proteins have been used for translational regulation, how to combine them, and how to design effective gene circuits.
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Affiliation(s)
- Hideyuki Nakanishi
- Department of Biofunction Research, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
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12
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Yang J, Ding S. Chimeric RNA-binding protein-based killing switch targeting hepatocellular carcinoma cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 25:683-695. [PMID: 34589286 PMCID: PMC8463442 DOI: 10.1016/j.omtn.2021.08.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 08/13/2021] [Indexed: 11/09/2022]
Abstract
Cancer cell-specific killing switches are synthetic circuits developed as an intelligent weapon to specifically eliminate malignant cells. RNA-delivered synthetic circuits provide safer means to control oncolytic functions, in which proteolysis-responding capsid-cNOT7 is developed to enable logic computation and modular design. Unfortunately, although circuits containing these capsid-cNOT7s exhibited good performance when introduced as replicons, in modified mRNA (modRNA) delivery, the performance was not quite as good. To improve this situation, alternative modules suitable for modRNA delivery need to be developed. An attractive option is RNA-binding protein (RBP)/riboswitches. In this study, RBPs were engineered by fusing with degron and cleavage sites. The compatibility of these chimeric RBPs with proteolysis-based sensing units were tested. Eight two-input logic gates and four three-input logic gates were implemented. After building this chimeric RBP-based system, we constructed a hepatocellular carcinoma (HCC) cell-specific killing circuit using two proteolysis-based sensing units, a two-input logic OR gate, and a leakproof apoptosis-inducing actuator, which distinguished HCC cells and induced apoptosis in a mixed IMR90-PLC/PRF/5 population.
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Affiliation(s)
- Jiong Yang
- Department of Gastroenterology, Peking University Third Hospital, Beijing 100191, China.,Beijing Key Laboratory for Helicobacter Pylori Infection and Upper Gastrointestinal Diseases, Beijing 100191, China
| | - Shigang Ding
- Department of Gastroenterology, Peking University Third Hospital, Beijing 100191, China.,Beijing Key Laboratory for Helicobacter Pylori Infection and Upper Gastrointestinal Diseases, Beijing 100191, China
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13
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Hong JC, Fan HC, Yang PJ, Lin DW, Wu HC, Huang HC. Localized Proteolysis for the Construction of Intracellular Asymmetry in Escherichia coli. ACS Synth Biol 2021; 10:1830-1836. [PMID: 34374512 DOI: 10.1021/acssynbio.1c00200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein-level regulations have gained importance in building synthetic circuits, as they offer a potential advantage in the speed of operation compared to gene regulation circuits. In nature, localized protein degradation is prevalent in polarizing cellular signaling. We, therefore, set out to systematically investigate whether localized proteolysis can be employed to construct intracellular asymmetry in Escherichia coli. We demonstrate that, by inserting a cognate cleavage site between the reporter and C-terminal degron, the unstable reporter can be stabilized in the presence of the tobacco etch virus protease. Furthermore, the split protease can be functionally reconstituted by the PopZ-based polarity system to exert localized proteolysis. Selective stabilization of the unstable reporter at the PopZ pole can lead to intracellular asymmetry in E. coli. Our study provides complementary evidence to support that localized proteolysis may be a strategy for polarization in developmental cell biology. Circuits designed in this study may also help to expand the synthetic biology repository for the engineering of synthetic morphogenesis, particularly for processes that require rapid control of local protein abundance.
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Affiliation(s)
- Jui-Chung Hong
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Hao-Chun Fan
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Po-Jiun Yang
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Da-Wei Lin
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Hsuan-Chen Wu
- Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan
| | - Hsiao-Chun Huang
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei 10617, Taiwan
- Graduate Institute of Electronics Engineering, National Taiwan University, Taipei 10617, Taiwan
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14
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Yang J, Ding S. Engineering L7Ae for RNA-Only Delivery Kill Switch Targeting CMS2 Type Colorectal Cancer Cells. ACS Synth Biol 2021; 10:1095-1105. [PMID: 33939419 DOI: 10.1021/acssynbio.0c00612] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The lack of specific-targeting therapy to precisely identify and kill malignant cells while sparing others is a great challenge in colorectal cancer (CRC) treatment. In the era of molecular classification of tumors, CRC has been grouped into four Consensus Molecular Subtypes. Accounting for 37% of all types, the CMS2 group (canonical type) shows distinguishing features: WNT and MYC signaling activation. In this study, we designed an RNA-only delivery kill switch to specifically eliminate CMS2 type CRC cells. The sensing and logic processing functions are integrated by the newly engineered L7Ae, which can not only detect the stability of β-catenin protein and the presence of cytoplasm located Myc/Myc-nick, but also do logic computation. The circuit specifically eliminated HCT-116 cells while sparing other kinds of cells, showing a proof-of-principle approach to precisely target CMS2 type CRC.
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Affiliation(s)
- Jiong Yang
- Department of Gastroenterology, Peking University Third Hospital, Beijing 100191, China
- Beijing Key Laboratory for Helicobacter pylori Infection and Upper Gastrointestinal Diseases, Beijing 100191, China
| | - Shigang Ding
- Department of Gastroenterology, Peking University Third Hospital, Beijing 100191, China
- Beijing Key Laboratory for Helicobacter pylori Infection and Upper Gastrointestinal Diseases, Beijing 100191, China
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15
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Stevens LM, Kim G, Koromila T, Steele JW, McGehee J, Stathopoulos A, Stein DS. Light-dependent N-end rule-mediated disruption of protein function in Saccharomyces cerevisiae and Drosophila melanogaster. PLoS Genet 2021; 17:e1009544. [PMID: 33999957 PMCID: PMC8158876 DOI: 10.1371/journal.pgen.1009544] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 05/27/2021] [Accepted: 04/12/2021] [Indexed: 12/12/2022] Open
Abstract
Here we describe the development and characterization of the photo-N-degron, a peptide tag that can be used in optogenetic studies of protein function in vivo. The photo-N-degron can be expressed as a genetic fusion to the amino termini of other proteins, where it undergoes a blue light-dependent conformational change that exposes a signal for the class of ubiquitin ligases, the N-recognins, which mediate the N-end rule mechanism of proteasomal degradation. We demonstrate that the photo-N-degron can be used to direct light-mediated degradation of proteins in Saccharomyces cerevisiae and Drosophila melanogaster with fine temporal control. In addition, we compare the effectiveness of the photo-N-degron with that of two other light-dependent degrons that have been developed in their abilities to mediate the loss of function of Cactus, a component of the dorsal-ventral patterning system in the Drosophila embryo. We find that like the photo-N-degron, the blue light-inducible degradation (B-LID) domain, a light-activated degron that must be placed at the carboxy terminus of targeted proteins, is also effective in eliciting light-dependent loss of Cactus function, as determined by embryonic dorsal-ventral patterning phenotypes. In contrast, another previously described photosensitive degron (psd), which also must be located at the carboxy terminus of associated proteins, has little effect on Cactus-dependent phenotypes in response to illumination of developing embryos. These and other observations indicate that care must be taken in the selection and application of light-dependent and other inducible degrons for use in studies of protein function in vivo, but importantly demonstrate that N- and C-terminal fusions to the photo-N-degron and the B-LID domain, respectively, support light-dependent degradation in vivo. Much of what we know about biological processes has come from the analysis of mutants whose loss-of-function phenotypes provide insight into their normal functions. However, for genes that are required for viability and which have multiple functions in the life of a cell or organism one can only observe mutant phenotypes produced up to the time of death. Normal functions performed in wild-type individuals later than the time of death of mutants cannot be observed. In one approach to overcoming this limitation, a class of peptide degradation signals (degrons) have been developed, which when fused to proteins-of-interest, can target those proteins for degradation in response to various stimuli (temperature, chemical agents, co-expressed proteins, or light). Here we describe a new inducible degron (the photo-N-degron or PND), which when fused to the N-terminus of a protein, can induce N-end rule-mediated degradation in response to blue-light illumination and have validated its use in both yeast and Drosophila embryos. Moreover, using the Drosophila embryonic patterning protein Cactus, we show that like the PND, the previously-described B-LID domain, but not the previously-described photosensitive degron (psd), can produce detectable light-inducible phenotypes in Drosophila embryos that are consistent with the role of Cactus in dorsal-ventral patterning.
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Affiliation(s)
- Leslie M. Stevens
- Department of Molecular Biosciences and Institute for Molecular and Cellular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Goheun Kim
- Department of Molecular Biosciences and Institute for Molecular and Cellular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Theodora Koromila
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - John W. Steele
- Department of Molecular Biosciences and Institute for Molecular and Cellular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - James McGehee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Angelike Stathopoulos
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (AS); (DSS)
| | - David S. Stein
- Department of Molecular Biosciences and Institute for Molecular and Cellular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail: (AS); (DSS)
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16
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Lovelett RJ, Zhao EM, Lalwani MA, Toettcher JE, Kevrekidis IG, L Avalos J. Dynamical Modeling of Optogenetic Circuits in Yeast for Metabolic Engineering Applications. ACS Synth Biol 2021; 10:219-227. [PMID: 33492138 PMCID: PMC10410538 DOI: 10.1021/acssynbio.0c00372] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dynamic control of engineered microbes using light via optogenetics has been demonstrated as an effective strategy for improving the yield of biofuels, chemicals, and other products. An advantage of using light to manipulate microbial metabolism is the relative simplicity of interfacing biological and computer systems, thereby enabling in silico control of the microbe. Using this strategy for control and optimization of product yield requires an understanding of how the microbe responds in real-time to the light inputs. Toward this end, we present mechanistic models of a set of yeast optogenetic circuits. We show how these models can predict short- and long-time response to varying light inputs and how they are amenable to use with model predictive control (the industry standard among advanced control algorithms). These models reveal dynamics characterized by time-scale separation of different circuit components that affect the steady and transient levels of the protein under control of the circuit. Ultimately, this work will help enable real-time control and optimization tools for improving yield and consistency in the production of biofuels and chemicals using microbial fermentations.
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Affiliation(s)
- Robert J Lovelett
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Evan M Zhao
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Makoto A Lalwani
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton, New Jersey 08544, United States
| | - Ioannis G Kevrekidis
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - José L Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- The Andlinger Center for Energy and the Environment, Princeton University, Princeton, New Jersey 08544, United States
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17
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Gaynor AS, Chen W. Conditional Protein Rescue by Binding-Induced Protective Shielding. ACS Synth Biol 2020; 9:2639-2647. [PMID: 33025786 DOI: 10.1021/acssynbio.0c00367] [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: 11/29/2022]
Abstract
Synthetic protein-level circuits offer an extra layer of cellular control on top of conventional gene-level circuits. Here, we describe a technology that allows conditional protein rescue (CPR) from proteasomal degradation using different protein inputs as masking agents. A target protein is fused to a degron tag and an affinity sensor domain. The use of nanobodies as the sensor domain offers a generalizable strategy to execute a wide range of protein-level circuits with ease. The utility of this new strategy was successfully demonstrated to distinguish cancer cells out of a healthy population using the HPV-specific E7 protein as a cellular marker. Because CPR can be programmed to execute more complex Boolean logic designs using cell-specific proteomes, this platform offers a highly modular and scalable framework for a wide range of applications based on synthetic protein circuits.
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Affiliation(s)
- Andrew S. Gaynor
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
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18
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On the cutting edge: protease-based methods for sensing and controlling cell biology. Nat Methods 2020; 17:885-896. [PMID: 32661424 DOI: 10.1038/s41592-020-0891-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 06/09/2020] [Indexed: 02/06/2023]
Abstract
Sequence-specific proteases have proven to be versatile building blocks for tools that report or control cellular function. Reporting methods link protease activity to biochemical signals, whereas control methods rely on engineering proteases to respond to exogenous inputs such as light or chemicals. In turn, proteases have inherent control abilities, as their native functions are to release, activate or destroy proteins by cleavage, with the irreversibility of proteolysis allowing sustained downstream effects. As a result, protease-based synthetic circuits have been created for diverse uses such as reporting cellular signaling, tuning protein expression, controlling viral replication and detecting cancer states. Here, we comprehensively review the development and application of protease-based methods for reporting and controlling cellular function in eukaryotes.
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19
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Vevea JD, Chapman ER. Acute disruption of the synaptic vesicle membrane protein synaptotagmin 1 using knockoff in mouse hippocampal neurons. eLife 2020; 9:56469. [PMID: 32515733 PMCID: PMC7282819 DOI: 10.7554/elife.56469] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 05/12/2020] [Indexed: 12/27/2022] Open
Abstract
The success of comparative cell biology for determining protein function relies on quality disruption techniques. Long-lived proteins, in postmitotic cells, are particularly difficult to eliminate. Moreover, cellular processes are notoriously adaptive; for example, neuronal synapses exhibit a high degree of plasticity. Ideally, protein disruption techniques should be both rapid and complete. Here, we describe knockoff, a generalizable method for the druggable control of membrane protein stability. We developed knockoff for neuronal use but show it also works in other cell types. Applying knockoff to synaptotagmin 1 (SYT1) results in acute disruption of this protein, resulting in loss of synchronous neurotransmitter release with a concomitant increase in the spontaneous release rate, measured optically. Thus, SYT1 is not only the proximal Ca2+ sensor for fast neurotransmitter release but also serves to clamp spontaneous release. Additionally, knockoff can be applied to protein domains as we show for another synaptic vesicle protein, synaptophysin 1.
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Affiliation(s)
- Jason D Vevea
- Department of Neuroscience, University of Wisconsin-Madison, Madison, United States.,Howard Hughes Medical Institute, Madison, United States
| | - Edwin R Chapman
- Department of Neuroscience, University of Wisconsin-Madison, Madison, United States.,Howard Hughes Medical Institute, Madison, United States
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20
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Gräwe A, Ranglack J, Weber W, Stein V. Engineering artificial signalling functions with proteases. Curr Opin Biotechnol 2020; 63:1-7. [DOI: 10.1016/j.copbio.2019.09.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/17/2019] [Accepted: 09/23/2019] [Indexed: 01/01/2023]
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21
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Fuchs M, Lohmann JU. Aiming for the top: non-cell autonomous control of shoot stem cells in Arabidopsis. JOURNAL OF PLANT RESEARCH 2020; 133:297-309. [PMID: 32146616 PMCID: PMC7214502 DOI: 10.1007/s10265-020-01174-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/27/2020] [Indexed: 05/13/2023]
Abstract
In multicellular organisms, not all cells are created equal. Instead, organismal complexity is achieved by specialisation and division of labour between distinct cell types. Therefore, the organism depends on the presence, correct proportion and function of all cell types. It follows that early development is geared towards setting up the basic body plan and to specify cell lineages. Since plants employ a post-embryonic mode of development, the continuous growth and addition of new organs require a source of new cells, as well as a strict regulation of cellular composition throughout the entire life-cycle. To meet these demands, evolution has brought about complex regulatory systems to maintain and control continuously active stem cell systems. Here, we review recent work on the mechanisms of non cell-autonomous control of shoot stem cells in the model plant Arabidopsis thaliana with a strong focus on the cell-to-cell mobility and function of the WUSCHEL homeodomain transcription factor.
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Affiliation(s)
- Michael Fuchs
- Department of Stem Cell Biology, Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Jan U Lohmann
- Department of Stem Cell Biology, Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany.
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22
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Wang F, Zhang R, Feng W, Tsuchiya D, Ballew O, Li J, Denic V, Lacefield S. Autophagy of an Amyloid-like Translational Repressor Regulates Meiotic Exit. Dev Cell 2020; 52:141-151.e5. [PMID: 31991104 DOI: 10.1016/j.devcel.2019.12.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 09/26/2019] [Accepted: 12/26/2019] [Indexed: 12/30/2022]
Abstract
We explored the potential for autophagy to regulate budding yeast meiosis. Following pre-meiotic DNA replication, we blocked autophagy by chemical inhibition of Atg1 kinase or engineered degradation of Atg14 and observed homologous chromosome segregation followed by sister chromatid separation; cells then underwent additional rounds of spindle formation and disassembly without DNA re-replication, leading to aberrant chromosome segregation. Analysis of cell-cycle regulators revealed that autophagy inhibition prevents meiosis II-specific expression of Clb3 and leads to the aberrant persistence of Clb1 and Cdc5, two substrates of a meiotic ubiquitin ligase activated by Ama1. Lastly, we found that during meiosis II, autophagy degrades Rim4, an amyloid-like translational repressor whose timed clearance regulates protein production from its mRNA targets, which include CLB3 and AMA1. Strikingly, engineered Clb3 or Ama1 production restored meiotic termination in the absence of autophagy. Thus, autophagy destroys a master regulator of meiotic gene expression to enable irreversible meiotic exit.
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Affiliation(s)
- Fei Wang
- Department of Internal Medicine, Center for Autophagy Research, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Rudian Zhang
- Department of Internal Medicine, Center for Autophagy Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Wenzhi Feng
- Department of Internal Medicine, Center for Autophagy Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Dai Tsuchiya
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Olivia Ballew
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Jiajia Li
- Department of Internal Medicine, Center for Autophagy Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Vladimir Denic
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
| | - Soni Lacefield
- Department of Biology, Indiana University, Bloomington, IN, USA.
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23
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Trauth J, Scheffer J, Hasenjäger S, Taxis C. Strategies to investigate protein turnover with fluorescent protein reporters in eukaryotic organisms. AIMS BIOPHYSICS 2020. [DOI: 10.3934/biophy.2020008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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24
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Chen RP, Gaynor AS, Chen W. Synthetic biology approaches for targeted protein degradation. Biotechnol Adv 2019; 37:107446. [DOI: 10.1016/j.biotechadv.2019.107446] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/03/2019] [Accepted: 09/06/2019] [Indexed: 12/12/2022]
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25
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Hasenjäger S, Trauth J, Hepp S, Goenrich J, Essen LO, Taxis C. Optogenetic Downregulation of Protein Levels with an Ultrasensitive Switch. ACS Synth Biol 2019; 8:1026-1036. [PMID: 30955324 DOI: 10.1021/acssynbio.8b00471] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Optogenetic control of protein activity is a versatile technique to gain control over cellular processes, for example, for biomedical and biotechnological applications. Among other techniques, the regulation of protein abundance by controlling either transcription or protein stability found common use as this controls the activity of any type of target protein. Here, we report modules of an improved variant of the photosensitive degron module and a light-sensitive transcription factor, which we compared to doxycycline-dependent transcriptional control. Given their modularity the combined control of synthesis and stability of a given target protein resulted in the synergistic down regulation of its abundance by light. This combined module exhibits very high switching ratios, profound downregulation of protein abundance at low light-fluxes, and fast protein depletion kinetics. Overall, this synergistic optogenetic multistep control (SOMCo) module is easy to implement and results in a regulation of protein abundance superior to each individual component.
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Affiliation(s)
- Sophia Hasenjäger
- Department of Biology/Genetics Philipps-University Marburg Karl-vom-Frisch-Straße 8, Marburg, 35032, Germany
| | - Jonathan Trauth
- Department of Biology/Genetics Philipps-University Marburg Karl-vom-Frisch-Straße 8, Marburg, 35032, Germany
- Department of Chemistry/Biochemistry Philipps-University Marburg Hans-Meerwein-Straße 4, Marburg, 35032, Germany
| | - Sebastian Hepp
- Department of Chemistry/Biochemistry Philipps-University Marburg Hans-Meerwein-Straße 4, Marburg, 35032, Germany
| | - Juri Goenrich
- Department of Biology/Genetics Philipps-University Marburg Karl-vom-Frisch-Straße 8, Marburg, 35032, Germany
| | - Lars-Oliver Essen
- Department of Chemistry/Biochemistry Philipps-University Marburg Hans-Meerwein-Straße 4, Marburg, 35032, Germany
| | - Christof Taxis
- Department of Biology/Genetics Philipps-University Marburg Karl-vom-Frisch-Straße 8, Marburg, 35032, Germany
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26
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Kats I, Khmelinskii A, Kschonsak M, Huber F, Knieß RA, Bartosik A, Knop M. Mapping Degradation Signals and Pathways in a Eukaryotic N-terminome. Mol Cell 2019; 70:488-501.e5. [PMID: 29727619 DOI: 10.1016/j.molcel.2018.03.033] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 01/26/2018] [Accepted: 03/27/2018] [Indexed: 01/01/2023]
Abstract
Most eukaryotic proteins are N-terminally acetylated. This modification can be recognized as a signal for selective protein degradation (degron) by the N-end rule pathways. However, the prevalence and specificity of such degrons in the proteome are unclear. Here, by systematically examining how protein turnover is affected by N-terminal sequences, we perform a comprehensive survey of degrons in the yeast N-terminome. We find that approximately 26% of nascent protein N termini encode cryptic degrons. These degrons exhibit high hydrophobicity and are frequently recognized by the E3 ubiquitin ligase Doa10, suggesting a role in protein quality control. In contrast, N-terminal acetylation rarely functions as a degron. Surprisingly, we identify two pathways where N-terminal acetylation has the opposite function and blocks protein degradation through the E3 ubiquitin ligase Ubr1. Our analysis highlights the complexity of N-terminal degrons and argues that hydrophobicity, not N-terminal acetylation, is the predominant feature of N-terminal degrons in nascent proteins.
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Affiliation(s)
- Ilia Kats
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Anton Khmelinskii
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Marc Kschonsak
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Florian Huber
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Robert A Knieß
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Anna Bartosik
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; Deutsches Krebsforschungszentrum (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
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27
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Gao XJ, Chong LS, Kim MS, Elowitz MB. Programmable protein circuits in living cells. Science 2018; 361:1252-1258. [PMID: 30237357 DOI: 10.1126/science.aat5062] [Citation(s) in RCA: 192] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 08/14/2018] [Indexed: 12/11/2022]
Abstract
Synthetic protein-level circuits could enable engineering of powerful new cellular behaviors. Rational protein circuit design would be facilitated by a composable protein-protein regulation system in which individual protein components can regulate one another to create a variety of different circuit architectures. In this study, we show that engineered viral proteases can function as composable protein components, which can together implement a broad variety of circuit-level functions in mammalian cells. In this system, termed CHOMP (circuits of hacked orthogonal modular proteases), input proteases dock with and cleave target proteases to inhibit their function. These components can be connected to generate regulatory cascades, binary logic gates, and dynamic analog signal-processing functions. To demonstrate the utility of this system, we rationally designed a circuit that induces cell death in response to upstream activators of the Ras oncogene. Because CHOMP circuits can perform complex functions yet be encoded as single transcripts and delivered without genomic integration, they offer a scalable platform to facilitate protein circuit engineering for biotechnological applications.
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Affiliation(s)
- Xiaojing J Gao
- Howard Hughes Medical Institute, Division of Biology and Biological Engineering, Broad Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Lucy S Chong
- Howard Hughes Medical Institute, Division of Biology and Biological Engineering, Broad Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Matthew S Kim
- Howard Hughes Medical Institute, Division of Biology and Biological Engineering, Broad Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Michael B Elowitz
- Howard Hughes Medical Institute, Division of Biology and Biological Engineering, Broad Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.
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28
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Lalwani MA, Zhao EM, Avalos JL. Current and future modalities of dynamic control in metabolic engineering. Curr Opin Biotechnol 2018; 52:56-65. [DOI: 10.1016/j.copbio.2018.02.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 02/11/2018] [Indexed: 12/30/2022]
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29
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Synthetic biology toolkits and applications in Saccharomyces cerevisiae. Biotechnol Adv 2018; 36:1870-1881. [PMID: 30031049 DOI: 10.1016/j.biotechadv.2018.07.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/10/2018] [Accepted: 07/16/2018] [Indexed: 12/26/2022]
Abstract
Synthetic biologists construct biological components and systems to look into biological phenomena and drive a myriad of practical applications that aim to tackle current global challenges in energy, healthcare and the environment. While most tools have been established in bacteria, particularly Escherichia coli, recent years have seen parallel developments in the model yeast strain Saccharomyces cerevisiae, one of the most well-understood eukaryotic biological system. Here, we outline the latest advances in yeast synthetic biology tools based on a framework of abstraction hierarchies of parts, circuits and genomes. In brief, the creation and characterization of biological parts are explored at the transcriptional, translational and post-translational levels. Using characterized parts as building block units, the designing of functional circuits is elaborated with examples. In addition, the status and potential applications of synthetic genomes as a genome level platform for biological system construction are also discussed. In addition to the development of a toolkit, we describe how those tools have been applied in the areas of drug production and screening, study of disease mechanisms, pollutant sensing and bioremediation. Finally, we provide a future outlook of yeast as a workhorse of eukaryotic genetics and a chosen chassis in this field.
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30
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Natsume T, Kanemaki MT. Conditional Degrons for Controlling Protein Expression at the Protein Level. Annu Rev Genet 2018; 51:83-102. [PMID: 29178817 DOI: 10.1146/annurev-genet-120116-024656] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The conditional depletion of a protein of interest (POI) is useful not only for loss-of-function studies, but also for the modulation of biological pathways. Technologies that work at the level of DNA, mRNA, and protein are available for temporal protein depletion. Compared with technologies targeting the pretranslation steps, direct protein depletion (or protein knockdown approaches) is advantageous in terms of specificity, reversibility, and time required for depletion, which can be achieved by fusing a POI with a protein domain called a degron that induces rapid proteolysis of the fusion protein. Conditional degrons can be activated or inhibited by temperature, small molecules, light, or the expression of another protein. The conditional degron-based technologies currently available are described and discussed.
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Affiliation(s)
- Toyoaki Natsume
- Division of Molecular Cell Engineering, National Institute of Genetics, Research Organization of Information and Systems (ROIS), and Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan;
| | - Masato T Kanemaki
- Division of Molecular Cell Engineering, National Institute of Genetics, Research Organization of Information and Systems (ROIS), and Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan;
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31
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Peng B, Nielsen LK, Kampranis SC, Vickers CE. Engineered protein degradation of farnesyl pyrophosphate synthase is an effective regulatory mechanism to increase monoterpene production in Saccharomyces cerevisiae. Metab Eng 2018; 47:83-93. [DOI: 10.1016/j.ymben.2018.02.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 02/02/2018] [Accepted: 02/14/2018] [Indexed: 10/18/2022]
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32
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Billerbeck S. Small Functional Peptides and Their Application in Superfunctionalizing Proteins. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Sonja Billerbeck
- Columbia University; Department of Chemistry; 550 West 120th Street New York NY 10027 USA
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Lauritsen I, Martínez V, Ronda C, Nielsen AT, Nørholm MHH. Bacterial Genome Editing Strategy for Control of Transcription and Protein Stability. Methods Mol Biol 2018; 1671:27-37. [PMID: 29170951 DOI: 10.1007/978-1-4939-7295-1_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In molecular biology and cell factory engineering, tools that enable control of protein production and stability are highly important. Here, we describe protocols for tagging genes in Escherichia coli allowing for inducible degradation and transcriptional control of any soluble protein of interest. The underlying molecular biology is based on the two cross-kingdom tools CRISPRi and the N-end rule for protein degradation. Genome editing is performed with the CRMAGE technology and randomization of the translational initiation region minimizes the polar effects of tag insertion. The approach has previously been applied for targeting proteins originating from essential operon-located genes and has potential to serve as a universal synthetic biology tool.
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Affiliation(s)
- Ida Lauritsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Anker Engelunds Vej 1, 2800, Kgs. Lyngby, Denmark
| | - Virginia Martínez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Anker Engelunds Vej 1, 2800, Kgs. Lyngby, Denmark
| | - Carlotta Ronda
- Systems and Synthetic Biology, Columbia University Medical Center, 3960 Broadway, New York, NY, 10032, USA
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Anker Engelunds Vej 1, 2800, Kgs. Lyngby, Denmark
| | - Morten H H Nørholm
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Anker Engelunds Vej 1, 2800, Kgs. Lyngby, Denmark.
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Martínez V, Lauritsen I, Hobel T, Li S, Nielsen AT, Nørholm M. CRISPR/Cas9-based genome editing for simultaneous interference with gene expression and protein stability. Nucleic Acids Res 2017; 45:e171. [PMID: 28981713 PMCID: PMC5714205 DOI: 10.1093/nar/gkx797] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 07/06/2017] [Accepted: 08/30/2017] [Indexed: 11/12/2022] Open
Abstract
Interference with genes is the foundation of reverse genetics and is key to manipulation of living cells for biomedical and biotechnological applications. However, classical genetic knockout and transcriptional knockdown technologies have different drawbacks and offer no control over existing protein levels. Here, we describe an efficient genome editing approach that affects specific protein abundances by changing the rates of both RNA synthesis and protein degradation, based on the two cross-kingdom control mechanisms CRISPRi and the N-end rule for protein stability. In addition, our approach demonstrates that CRISPRi efficiency is dependent on endogenous gene expression levels. The method has broad applications in e.g. study of essential genes and antibiotics discovery.
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Affiliation(s)
- Virginia Martínez
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Ida Lauritsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Tonja Hobel
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Songyuan Li
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Alex Toftgaard Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Morten H. H. Nørholm
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
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Oesterle S, Roberts TM, Widmer LA, Mustafa H, Panke S, Billerbeck S. Sequence-based prediction of permissive stretches for internal protein tagging and knockdown. BMC Biol 2017; 15:100. [PMID: 29084520 PMCID: PMC5661948 DOI: 10.1186/s12915-017-0440-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/11/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Internal tagging of proteins by inserting small functional peptides into surface accessible permissive sites has proven to be an indispensable tool for basic and applied science. Permissive sites are typically identified by transposon mutagenesis on a case-by-case basis, limiting scalability and their exploitation as a system-wide protein engineering tool. METHODS We developed an apporach for predicting permissive stretches (PSs) in proteins based on the identification of length-variable regions (regions containing indels) in homologous proteins. RESULTS We verify that a protein's primary structure information alone is sufficient to identify PSs. Identified PSs are predicted to be predominantly surface accessible; hence, the position of inserted peptides is likely suitable for diverse applications. We demonstrate the viability of this approach by inserting a Tobacco etch virus protease recognition site (TEV-tag) into several PSs in a wide range of proteins, from small monomeric enzymes (adenylate kinase) to large multi-subunit molecular machines (ATP synthase) and verify their functionality after insertion. We apply this method to engineer conditional protein knockdowns directly in the Escherichia coli chromosome and generate a cell-free platform with enhanced nucleotide stability. CONCLUSIONS Functional internally tagged proteins can be rationally designed and directly chromosomally implemented. Critical for the successful design of protein knockdowns was the incorporation of surface accessibility and secondary structure predictions, as well as the design of an improved TEV-tag that enables efficient hydrolysis when inserted into the middle of a protein. This versatile and portable approach can likely be adapted for other applications, and broadly adopted. We provide guidelines for the design of internally tagged proteins in order to empower scientists with little or no protein engineering expertise to internally tag their target proteins.
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Affiliation(s)
- Sabine Oesterle
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Tania Michelle Roberts
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Lukas Andreas Widmer
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
- Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058, Basel, Switzerland
- Life Science Zürich Graduate School in Systems Biology, Zürich, Switzerland
| | - Harun Mustafa
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
- Department of Computer Science, ETH Zürich, Zürich, Switzerland
| | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Sonja Billerbeck
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland.
- Present address: Chemistry Department, Columbia University, 550 West 120th Street, New York, NY, 10027, USA.
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36
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Kanca O, Bellen HJ, Schnorrer F. Gene Tagging Strategies To Assess Protein Expression, Localization, and Function in Drosophila. Genetics 2017; 207:389-412. [PMID: 28978772 PMCID: PMC5629313 DOI: 10.1534/genetics.117.199968] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 06/13/2017] [Indexed: 01/15/2023] Open
Abstract
Analysis of gene function in complex organisms relies extensively on tools to detect the cellular and subcellular localization of gene products, especially proteins. Typically, immunostaining with antibodies provides these data. However, due to cost, time, and labor limitations, generating specific antibodies against all proteins of a complex organism is not feasible. Furthermore, antibodies do not enable live imaging studies of protein dynamics. Hence, tagging genes with standardized immunoepitopes or fluorescent tags that permit live imaging has become popular. Importantly, tagging genes present in large genomic clones or at their endogenous locus often reports proper expression, subcellular localization, and dynamics of the encoded protein. Moreover, these tagging approaches allow the generation of elegant protein removal strategies, standardization of visualization protocols, and permit protein interaction studies using mass spectrometry. Here, we summarize available genomic resources and techniques to tag genes and discuss relevant applications that are rarely, if at all, possible with antibodies.
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Affiliation(s)
- Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas 77030
- Howard Hughes Medical Institute, Houston, Texas 77030
| | - Frank Schnorrer
- Developmental Biology Institute of Marseille (IBDM), UMR 7288, CNRS, Aix-Marseille Université, 13288, France
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Wong J, Chen X, Truong K. Engineering a temperature sensitive tobacco etch virus protease. Protein Eng Des Sel 2017; 30:705-712. [PMID: 29040785 DOI: 10.1093/protein/gzx050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 08/26/2017] [Indexed: 11/12/2022] Open
Abstract
Since tobacco etch virus protease (TEVp) has a high specificity and efficiency in cleaving its target substrates, many groups have attempted to engineer conditional control of its activity. Temperature induction is widely used for modulating gene function because it has fast temporal response, good penetrability and applicability to many model organisms. Here, we engineered a temperature sensitive TEVp (tsTEVp) by using N-terminal truncations to TEVp that achieved efficient proteolysis on a timescale of 4 h after 30°C induction, while remaining relatively inactive at 37°C. As demonstration, tsTEVp was used to generate temperature-induced biological responses for protein translocation, protein degradation and Ca2+-mediated cellular blebbing. Lastly, tsTEVp and their engineered target substrates could find applications in engineered synthetic biological systems.
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Affiliation(s)
- J Wong
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, Canada M5S 3G9
| | - X Chen
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, Canada M5S 3G9
| | - K Truong
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, Canada M5S 3G9.,Edward S. Rogers, Sr. Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Circle, Toronto, Ontario, Canada M5S 3G4
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38
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Affiliation(s)
- George M. Burslem
- Departments of Molecular,
Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, 219 Prospect Street, New Haven, Connecticut 06511, United States
| | - Craig M. Crews
- Departments of Molecular,
Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, 219 Prospect Street, New Haven, Connecticut 06511, United States
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39
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Powers BL, Hall MC. Re-examining the role of Cdc14 phosphatase in reversal of Cdk phosphorylation during mitotic exit. J Cell Sci 2017; 130:2673-2681. [PMID: 28663385 DOI: 10.1242/jcs.201012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 06/26/2017] [Indexed: 01/12/2023] Open
Abstract
Inactivation of cyclin-dependent kinase (Cdk) and reversal of Cdk phosphorylation are universally required for mitotic exit. In budding yeast (Saccharomyces cerevisiae), Cdc14 is essential for both and thought to be the major Cdk-counteracting phosphatase. However, Cdc14 is not required for mitotic exit in many eukaryotes, despite highly conserved biochemical properties. The question of how similar enzymes could have such disparate influences on mitotic exit prompted us to re-examine the contribution of budding yeast Cdc14. By using an auxin-inducible degron, we show that severe Cdc14 depletion has no effect on the kinetics of mitotic exit and bulk Cdk substrate dephosphorylation, but causes a cell separation defect and is ultimately lethal. Phosphoproteomic analysis revealed that Cdc14 is highly selective for distinct Cdk sites in vivo and does not catalyze widespread Cdk substrate dephosphorylation. We conclude that additional phosphatases likely contribute substantially to Cdk substrate dephosphorylation and coordination of mitotic exit in budding yeast, similar to in other eukaryotes, and the critical mitotic exit functions of Cdc14 require trace amounts of enzyme. We propose that Cdc14 plays very specific, and often different, roles in counteracting Cdk phosphorylation in all species.
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Affiliation(s)
- Brendan L Powers
- Department of Biochemistry and Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Mark C Hall
- Department of Biochemistry and Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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40
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Targeting protein function: the expanding toolkit for conditional disruption. Biochem J 2017; 473:2573-89. [PMID: 27574023 PMCID: PMC5003692 DOI: 10.1042/bcj20160240] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/20/2016] [Indexed: 01/06/2023]
Abstract
A major objective in biological research is to understand spatial and temporal requirements for any given gene, especially in dynamic processes acting over short periods, such as catalytically driven reactions, subcellular transport, cell division, cell rearrangement and cell migration. The interrogation of such processes requires the use of rapid and flexible methods of interfering with gene function. However, many of the most widely used interventional approaches, such as RNAi or CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 (CRISPR-associated 9), operate at the level of the gene or its transcripts, meaning that the effects of gene perturbation are exhibited over longer time frames than the process under investigation. There has been much activity over the last few years to address this fundamental problem. In the present review, we describe recent advances in disruption technologies acting at the level of the expressed protein, involving inducible methods of protein cleavage, (in)activation, protein sequestration or degradation. Drawing on examples from model organisms we illustrate the utility of fast-acting techniques and discuss how different components of the molecular toolkit can be employed to dissect previously intractable biochemical processes and cellular behaviours.
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41
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Lucas X, Ciulli A. Recognition of substrate degrons by E3 ubiquitin ligases and modulation by small-molecule mimicry strategies. Curr Opin Struct Biol 2017; 44:101-110. [DOI: 10.1016/j.sbi.2016.12.015] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/12/2016] [Accepted: 12/16/2016] [Indexed: 12/11/2022]
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The Mitotic Exit Network Regulates Spindle Pole Body Selection During Sporulation of Saccharomyces cerevisiae. Genetics 2017; 206:919-937. [PMID: 28450458 DOI: 10.1534/genetics.116.194522] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 04/11/2017] [Indexed: 01/11/2023] Open
Abstract
Age-based inheritance of centrosomes in eukaryotic cells is associated with faithful chromosome distribution in asymmetric cell divisions. During Saccharomyces cerevisiae ascospore formation, such an inheritance mechanism targets the yeast centrosome equivalents, the spindle pole bodies (SPBs) at meiosis II onset. Decreased nutrient availability causes initiation of spore formation at only the younger SPBs and their associated genomes. This mechanism ensures encapsulation of nonsister genomes, which preserves genetic diversity and provides a fitness advantage at the population level. Here, by usage of an enhanced system for sporulation-induced protein depletion, we demonstrate that the core mitotic exit network (MEN) is involved in age-based SPB selection. Moreover, efficient genome inheritance requires Dbf2/20-Mob1 during a late step in spore maturation. We provide evidence that the meiotic functions of the MEN are more complex than previously thought. In contrast to mitosis, completion of the meiotic divisions does not strictly rely on the MEN whereas its activity is required at different time points during spore development. This is reminiscent of vegetative MEN functions in spindle polarity establishment, mitotic exit, and cytokinesis. In summary, our investigation contributes to the understanding of age-based SPB inheritance during sporulation of S. cerevisiae and provides general insights on network plasticity in the context of a specialized developmental program. Moreover, the improved system for a developmental-specific tool to induce protein depletion will be useful in other biological contexts.
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Taxis C. Development of a Synthetic Switch to Control Protein Stability in Eukaryotic Cells with Light. Methods Mol Biol 2017; 1596:241-255. [PMID: 28293891 DOI: 10.1007/978-1-4939-6940-1_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In eukaryotic cells, virtually all regulatory processes are influenced by proteolysis. Thus, synthetic control of protein stability is a powerful approach to influence cellular behavior. To achieve this, selected target proteins are modified with a conditional degradation sequence (degron) that responds to a distinct signal. For development of a synthetic degron, an appropriate sensor domain is fused with a degron such that activity of the degron is under control of the sensor. This chapter describes the development of a light-activated, synthetic degron in the model organism Saccharomyces cerevisiae. This photosensitive degron module is composed of the light-oxygen-voltage (LOV) 2 photoreceptor domain of Arabidopsis thaliana phototropin 1 and a degron derived from murine ornithine decarboxylase (ODC). Excitation of the photoreceptor with blue light induces a conformational change that leads to exposure and activation of the degron. Subsequently, the protein is targeted for degradation by the proteasome. Here, the strategy for degron module development and optimization is described in detail together with experimental aspects, which were pivotal for successful implementation of light-controlled proteolysis. The engineering of the photosensitive degron (psd) module may well serve as a blueprint for future development of sophisticated synthetic switches.
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Affiliation(s)
- Christof Taxis
- Department of Biology/Genetics, Philipps-Universität Marburg, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany.
- Department of Chemistry/Biochemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35043, Marburg, Germany.
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44
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Going native: Complete removal of protein purification affinity tags by simple modification of existing tags and proteases. Protein Expr Purif 2017; 129:18-24. [DOI: 10.1016/j.pep.2016.09.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 08/18/2016] [Accepted: 09/05/2016] [Indexed: 11/17/2022]
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45
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Faden F, Ramezani T, Mielke S, Almudi I, Nairz K, Froehlich MS, Höckendorff J, Brandt W, Hoehenwarter W, Dohmen RJ, Schnittger A, Dissmeyer N. Phenotypes on demand via switchable target protein degradation in multicellular organisms. Nat Commun 2016; 7:12202. [PMID: 27447739 PMCID: PMC4961840 DOI: 10.1038/ncomms12202] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 06/10/2016] [Indexed: 12/20/2022] Open
Abstract
Phenotypes on-demand generated by controlling activation and accumulation of proteins of interest are invaluable tools to analyse and engineer biological processes. While temperature-sensitive alleles are frequently used as conditional mutants in microorganisms, they are usually difficult to identify in multicellular species. Here we present a versatile and transferable, genetically stable system based on a low-temperature-controlled N-terminal degradation signal (lt-degron) that allows reversible and switch-like tuning of protein levels under physiological conditions in vivo. Thereby, developmental effects can be triggered and phenotypes on demand generated. The lt-degron was established to produce conditional and cell-type-specific phenotypes and is generally applicable in a wide range of organisms, from eukaryotic microorganisms to plants and poikilothermic animals. We have successfully applied this system to control the abundance and function of transcription factors and different enzymes by tunable protein accumulation.
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Affiliation(s)
- Frederik Faden
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, D-06120 Halle (Saale), Germany
- ScienceCampus Halle—Plant-based Bioeconomy, Betty-Heimann-Strasse 3, D-06120 Halle (Saale), Germany
| | - Thomas Ramezani
- University Group at the Max Planck Institute for Plant Breeding Research (MPIPZ), Max Delbrück Laboratory, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany
- University of Cologne, Institute of Botany III, Biocenter, Zülpicher Str. 47 b, D-50674 Cologne, Germany
| | - Stefan Mielke
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, D-06120 Halle (Saale), Germany
- ScienceCampus Halle—Plant-based Bioeconomy, Betty-Heimann-Strasse 3, D-06120 Halle (Saale), Germany
| | - Isabel Almudi
- Institute of Molecular Systems Biology (IMSB), Swiss Federal Institute of Technology (ETH), Wolfgang-Pauli-Strasse 16, CH-8093 Zurich, Switzerland
| | - Knud Nairz
- Institute of Molecular Systems Biology (IMSB), Swiss Federal Institute of Technology (ETH), Wolfgang-Pauli-Strasse 16, CH-8093 Zurich, Switzerland
| | - Marceli S. Froehlich
- Institute for Genetics, Biocenter, University of Cologne, Zülpicher Straße 47a, D-50674 Cologne, Germany
| | - Jörg Höckendorff
- Institute for Genetics, Biocenter, University of Cologne, Zülpicher Straße 47a, D-50674 Cologne, Germany
| | - Wolfgang Brandt
- Computational Chemistry, Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, D-06120 Halle (Saale), Germany
| | - Wolfgang Hoehenwarter
- Proteomics Unit, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, Halle (Saale) D-06120, Germany
| | - R. Jürgen Dohmen
- Institute for Genetics, Biocenter, University of Cologne, Zülpicher Straße 47a, D-50674 Cologne, Germany
| | - Arp Schnittger
- University Group at the Max Planck Institute for Plant Breeding Research (MPIPZ), Max Delbrück Laboratory, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany
- University of Cologne, Institute of Botany III, Biocenter, Zülpicher Str. 47 b, D-50674 Cologne, Germany
- Département Mécanismes Moléculaires de la Plasticité Phénotypique, Institut de Biologie Moléculaire des Plantes du CNRS, IBMP-CNRS, Unité Propre de Recherche 2357, Conventionné avec l'Université de Strasbourg, 12, rue du Général Zimmer, Strasbourg F-67000, France
| | - Nico Dissmeyer
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, D-06120 Halle (Saale), Germany
- ScienceCampus Halle—Plant-based Bioeconomy, Betty-Heimann-Strasse 3, D-06120 Halle (Saale), Germany
- University Group at the Max Planck Institute for Plant Breeding Research (MPIPZ), Max Delbrück Laboratory, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany
- University of Cologne, Institute of Botany III, Biocenter, Zülpicher Str. 47 b, D-50674 Cologne, Germany
- Département Mécanismes Moléculaires de la Plasticité Phénotypique, Institut de Biologie Moléculaire des Plantes du CNRS, IBMP-CNRS, Unité Propre de Recherche 2357, Conventionné avec l'Université de Strasbourg, 12, rue du Général Zimmer, Strasbourg F-67000, France
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Fernandez-Rodriguez J, Voigt CA. Post-translational control of genetic circuits using Potyvirus proteases. Nucleic Acids Res 2016; 44:6493-502. [PMID: 27298256 PMCID: PMC5291274 DOI: 10.1093/nar/gkw537] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 06/06/2016] [Indexed: 12/25/2022] Open
Abstract
Genetic engineering projects often require control over when a protein is degraded. To this end, we use a fusion between a degron and an inactivating peptide that can be added to the N-terminus of a protein. When the corresponding protease is expressed, it cleaves the peptide and the protein is degraded. Three protease:cleavage site pairs from Potyvirus are shown to be orthogonal and active in exposing degrons, releasing inhibitory domains and cleaving polyproteins. This toolbox is applied to the design of genetic circuits as a means to control regulator activity and degradation. First, we demonstrate that a gate can be constructed by constitutively expressing an inactivated repressor and having an input promoter drive the expression of the protease. It is also shown that the proteolytic release of an inhibitory domain can improve the dynamic range of a transcriptional gate (200-fold repression). Next, we design polyproteins containing multiple repressors and show that their cleavage can be used to control multiple outputs. Finally, we demonstrate that the dynamic range of an output can be improved (8-fold to 190-fold) with the addition of a protease-cleaved degron. Thus, controllable proteolysis offers a powerful tool for modulating and expanding the function of synthetic gene circuits.
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Affiliation(s)
- Jesus Fernandez-Rodriguez
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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47
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Vanella R, Callari R, Weston A, Heider H, Schwab MS, Kübler E. Yeast-based assays for screening 11β-HSD1 inhibitors. Microb Cell Fact 2016; 15:52. [PMID: 26980090 PMCID: PMC4791775 DOI: 10.1186/s12934-016-0450-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/07/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Intracellular metabolism of glucocorticoid hormones plays an important role in the pathogenesis of metabolic syndrome and regulates, among many physiological processes, collagen metabolism in skin. At the peripheral level the concentration of active glucocorticoids is mainly regulated by the 11β-hydroxysteroid dehydrogenase 1 (11β-HSD1) enzyme, involved in the conversion of cortisone into the biologically active hormone cortisol. Cortisol interacts with the glucocorticoid receptor and regulates the expression of different classes of genes within the nucleus. Due to its implication in glucocorticoid metabolism, the inhibition of 11β-HSD1 activity has become a dominant strategy for the treatment of metabolic syndrome. Moreover, inhibitors of this target enzyme can be used for development of formulations to counteract skin ageing. Here we present the construction of two yeast cell based assays that can be used for the screening of novel 11β-HSD1 inhibitors. RESULTS The yeast Saccharomyces cerevisiae is used as a host organism for the expression of human 11β-HSD1 as well as a genetically encoded assay system that allows intracellular screening of molecules with 11β-HSD1 inhibitory activity. As proof of concept the correlation between 11β-HSD1 inhibition and fluorescent output signals was successfully tested with increasing concentrations of carbenoxolone and tanshinone IIA, two known 11β-HSD1 inhibitors. The first assay detects a decrease in fluorescence upon 11β-HSD1 inhibition, whereas the second assay relies on stabilization of yEGFP upon inhibition of 11β-HSD1, resulting in a positive read-out and thus minimizing the rate of false positives sometimes associated with read-outs based on loss of signals. Specific inhibition of the ABC transporter Pdr5p improves the sensitivity of the assay strains to cortisone concentrations by up to 60 times. CONCLUSIONS Our yeast assay strains provide a cost-efficient and easy to handle alternative to other currently available assays for the screening of 11β-HSD1 inhibitors. These assays are designed for an initial fast screening of large numbers of compounds and enable the selection of cell permeable molecules with target inhibitory activity, before proceeding to more advanced selection processes. Moreover, they can be employed in yeast synthetic biology platforms to reconstitute heterologous biosynthetic pathways of drug-relevant scaffolds for simultaneous synthesis and screening of 11β-HSD1 inhibitors at intracellular level.
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Affiliation(s)
- Rosario Vanella
- />University of Applied Sciences Northwestern Switzerland, Gründenstrasse 40, 4132 Muttenz, Switzerland
| | - Roberta Callari
- />University of Applied Sciences Northwestern Switzerland, Gründenstrasse 40, 4132 Muttenz, Switzerland
- />Evolva SA, Duggingerstrasse 23, 4153 Reinach, Switzerland
| | - Anna Weston
- />University of Applied Sciences Northwestern Switzerland, Gründenstrasse 40, 4132 Muttenz, Switzerland
| | - Harald Heider
- />Evolva SA, Duggingerstrasse 23, 4153 Reinach, Switzerland
| | | | - Eric Kübler
- />University of Applied Sciences Northwestern Switzerland, Gründenstrasse 40, 4132 Muttenz, Switzerland
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48
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Sekar K, Gentile AM, Bostick JW, Tyo KEJ. N-Terminal-Based Targeted, Inducible Protein Degradation in Escherichia coli. PLoS One 2016; 11:e0149746. [PMID: 26900850 PMCID: PMC4765774 DOI: 10.1371/journal.pone.0149746] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 02/04/2016] [Indexed: 11/18/2022] Open
Abstract
Dynamically altering protein concentration is a central activity in synthetic biology. While many tools are available to modulate protein concentration by altering protein synthesis rate, methods for decreasing protein concentration by inactivation or degradation rate are just being realized. Altering protein synthesis rates can quickly increase the concentration of a protein but not decrease, as residual protein will remain for a while. Inducible, targeted protein degradation is an attractive option and some tools have been introduced for higher organisms and bacteria. Current bacterial tools rely on C-terminal fusions, so we have developed an N-terminal fusion (Ntag) strategy to increase the possible proteins that can be targeted. We demonstrate Ntag dependent degradation of mCherry and beta-galactosidase and reconfigure the Ntag system to perform dynamic, exogenously inducible degradation of a targeted protein and complement protein depletion by traditional synthesis repression. Model driven analysis that focused on rates, rather than concentrations, was critical to understanding and engineering the system. We expect this tool and our model to enable inducible protein degradation use particularly in metabolic engineering, biological study of essential proteins, and protein circuits.
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Affiliation(s)
- Karthik Sekar
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States of America
| | - Andrew M. Gentile
- Master of Biotechnology Program, Northwestern University, Evanston, IL, United States of America
| | - John W. Bostick
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States of America
- Department of Pathology, Northwestern University, Chicago, IL, United States of America
- Department of Microbiology-Immunology, Northwestern University, Chicago, IL, United States of America
| | - Keith E. J. Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States of America
- * E-mail:
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Naumann C, Mot AC, Dissmeyer N. Generation of Artificial N-end Rule Substrate Proteins In Vivo and In Vitro. Methods Mol Biol 2016; 1450:55-83. [PMID: 27424746 DOI: 10.1007/978-1-4939-3759-2_6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In order to determine the stability of a protein or protein fragment dependent on its N-terminal amino acid, and therefore relate its half-life to the N-end rule pathway of targeted protein degradation (NERD), non-Methionine (Met) amino acids need to be exposed at their amino terminal in most cases. Per definition, at this position, destabilizing residues are generally unlikely to occur without further posttranslational modification of immature (pre-)proproteins. Moreover, almost exclusively, stabilizing, or not per se destabilizing residues are N-terminally exposed upon Met excision by Met aminopeptidases. To date, there exist two prominent protocols to study the impact of destabilizing residues at the N-terminal of a given protein by selectively exposing the amino acid residue to be tested. Such proteins can be used to study NERD substrate candidates and analyze NERD enzymatic components. Namely, the well-established ubiquitin fusion technique (UFT) is used in vivo or in cell-free transcription/translation systems in vitro to produce a desired N-terminal residue in a protein of interest, whereas the proteolytic cleavage of recombinant fusion proteins by tobacco etch virus (TEV) protease is used in vitro to purify proteins with distinct N-termini. Here, we discuss how to accomplish in vivo and in vitro expression and modification of NERD substrate proteins that may be used as stability tester or activity reporter proteins and to characterize potential NERD substrates.The methods to generate artificial substrates via UFT or TEV cleavage are described here and can be used either in vivo in the context of stably transformed plants and cell culture expressing chimeric constructs or in vitro in cell-free systems such as rabbit reticulocyte lysate as well as after expression and purification of recombinant proteins from various hosts.
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Affiliation(s)
- Christin Naumann
- Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany.,ScienceCampus Halle - Plant-Based Bioeconomy, Halle (Saale), Germany
| | - Augustin C Mot
- Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany.,ScienceCampus Halle - Plant-Based Bioeconomy, Halle (Saale), Germany.,Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, Cluj-Napoca, Romania
| | - Nico Dissmeyer
- Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany. .,ScienceCampus Halle - Plant-Based Bioeconomy, Halle (Saale), Germany.
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50
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Morgado G, Gerngross D, Roberts TM, Panke S. Synthetic Biology for Cell-Free Biosynthesis: Fundamentals of Designing Novel In Vitro Multi-Enzyme Reaction Networks. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 162:117-146. [PMID: 27757475 DOI: 10.1007/10_2016_13] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cell-free biosynthesis in the form of in vitro multi-enzyme reaction networks or enzyme cascade reactions emerges as a promising tool to carry out complex catalysis in one-step, one-vessel settings. It combines the advantages of well-established in vitro biocatalysis with the power of multi-step in vivo pathways. Such cascades have been successfully applied to the synthesis of fine and bulk chemicals, monomers and complex polymers of chemical importance, and energy molecules from renewable resources as well as electricity. The scale of these initial attempts remains small, suggesting that more robust control of such systems and more efficient optimization are currently major bottlenecks. To this end, the very nature of enzyme cascade reactions as multi-membered systems requires novel approaches for implementation and optimization, some of which can be obtained from in vivo disciplines (such as pathway refactoring and DNA assembly), and some of which can be built on the unique, cell-free properties of cascade reactions (such as easy analytical access to all system intermediates to facilitate modeling).
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Affiliation(s)
- Gaspar Morgado
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Daniel Gerngross
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Tania M Roberts
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Sven Panke
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.
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