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Verbič A, Lebar T, Praznik A, Jerala R. Correction to Subunits of E3 Ligase Complex as Degrons for Efficient Degradation of Cytosolic, Nuclear and Membrane Proteins. ACS Synth Biol 2024. [PMID: 38678638 DOI: 10.1021/acssynbio.4c00257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Affiliation(s)
- Anže Verbič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
- Interdisciplinary Doctoral Study of Biomedicine, Medical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Tina Lebar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Arne Praznik
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Snoj J, Lapenta F, Jerala R. Preorganized cyclic modules facilitate the self-assembly of protein nanostructures. Chem Sci 2024; 15:3673-3686. [PMID: 38455016 PMCID: PMC10915844 DOI: 10.1039/d3sc06658d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/15/2024] [Indexed: 03/09/2024] Open
Abstract
The rational design of supramolecular assemblies aims to generate complex systems based on the simple information encoded in the chemical structure. Programmable molecules such as nucleic acids and polypeptides are particularly suitable for designing diverse assemblies and shapes not found in nature. Here, we describe a strategy for assembling modular architectures based on structurally and covalently preorganized subunits. Cyclization through spontaneous self-splicing of split intein and coiled-coil dimer-based interactions of polypeptide chains provide structural constraints, facilitating the desired assembly. We demonstrate the implementation of a strategy based on the preorganization of the subunits by designing a two-chain coiled-coil protein origami (CCPO) assembly that adopts a tetrahedral topology only when one or both subunit chains are covalently cyclized. Employing this strategy, we further design a 109 kDa trimeric CCPO assembly comprising 24 CC-forming segments. In this case, intein cyclization was crucial for the assembly of a concave octahedral scaffold, a newly designed protein fold. The study highlights the importance of preorganization of building modules to facilitate the self-assembly of higher-order supramolecular structures.
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Affiliation(s)
- Jaka Snoj
- Department of Synthetic Biology and Immunology, National Institute of Chemistry Hajdrihova 19 SI-1000 Ljubljana Slovenia
- Interdisciplinary Doctoral Program in Biomedicine, University of Ljubljana Kongresni trg 12 SI-1000 Ljubljana Slovenia
| | - Fabio Lapenta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry Hajdrihova 19 SI-1000 Ljubljana Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry Hajdrihova 19 SI-1000 Ljubljana Slovenia
- EN-FIST Centre of Excellence Trg OF 13 SI-1000 Ljubljana Slovenia
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Govednik T, Lainšček D, Kuhar U, Lachish M, Janežič S, Štrbenc M, Krapež U, Jerala R, Atlas D, Manček-Keber M. TXM peptides inhibit SARS-CoV-2 infection, syncytia formation, and lower inflammatory consequences. Antiviral Res 2024; 222:105806. [PMID: 38211737 DOI: 10.1016/j.antiviral.2024.105806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 12/23/2023] [Accepted: 01/08/2024] [Indexed: 01/13/2024]
Abstract
After three years of the SARS-CoV-2 pandemic, the search and availability of relatively low-cost benchtop therapeutics for people not at high risk for a severe disease are still ongoing. Although vaccines and new SARS-CoV-2 variants reduce the death toll, the long COVID-19 along with neurologic symptoms can develop and persist even after a mild initial infection. Reinfections, which further increase the risk of sequelae in multiple organ systems as well as the risk of death, continue to require caution. The spike protein of SARS-CoV-2 is an important target for both vaccines and therapeutics. The presence of disulfide bonds in the receptor binding domain (RBD) of the spike protein is essential for its binding to the human ACE2 receptor and cell entry. Here, we demonstrate that thiol-reducing peptides based on the active site of oxidoreductase thioredoxin 1, called thioredoxin mimetic (TXM) peptides, can prevent syncytia formation, SARS-CoV-2 entry into cells, and infection in a mouse model. We also show that TXM peptides inhibit the redox-sensitive HIV pseudotyped viral cell entry. These results support disulfide targeting as a common therapeutic strategy for treating infections caused by viruses using redox-sensitive fusion. Furthermore, TXM peptides exert anti-inflammatory properties by lowering the activation of NF-κB and IRF signaling pathways, mitogen-activated protein kinases (MAPKs) and lipopolysaccharide (LPS)-induced cytokines in mice. The antioxidant and anti-inflammatory effects of the TXM peptides, which also cross the blood-brain barrier, in combination with prevention of viral infections, may provide a beneficial clinical strategy to lower viral infections and mitigate severe consequences of COVID-19.
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Affiliation(s)
- Tea Govednik
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000, Ljubljana, Slovenia; Graduate School of Biomedicine, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Duško Lainšček
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000, Ljubljana, Slovenia; Centre of Excellence EN-FIST, 1000, Ljubljana, Slovenia
| | - Urška Kuhar
- Institute for Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Marva Lachish
- Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Sandra Janežič
- National Laboratory of Health, Environment and Food, 2000, Maribor, Slovenia
| | - Malan Štrbenc
- Institute for Preclinical Sciences, Veterinary Faculty, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Uroš Krapež
- Institute of Poultry, Birds, Small Mammals and Reptiles, Veterinary Faculty, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000, Ljubljana, Slovenia; Centre of Excellence EN-FIST, 1000, Ljubljana, Slovenia
| | - Daphne Atlas
- Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
| | - Mateja Manček-Keber
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000, Ljubljana, Slovenia; Centre of Excellence EN-FIST, 1000, Ljubljana, Slovenia.
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Plaper T, Merljak E, Fink T, Satler T, Ljubetič A, Lainšček D, Jazbec V, Benčina M, Stevanoska S, Džeroski S, Jerala R. Designed allosteric protein logic. Cell Discov 2024; 10:8. [PMID: 38228615 DOI: 10.1038/s41421-023-00635-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 12/03/2023] [Indexed: 01/18/2024] Open
Abstract
The regulation of protein function by external or internal signals is one of the key features of living organisms. The ability to directly control the function of a selected protein would represent a valuable tool for regulating biological processes. Here, we present a generally applicable regulation of proteins called INSRTR, based on inserting a peptide into a loop of a target protein that retains its function. We demonstrate the versatility and robustness of coiled-coil-mediated regulation, which enables designs for either inactivation or activation of selected protein functions, and implementation of two-input logic functions with rapid response in mammalian cells. The selection of insertion positions in tested proteins was facilitated by using a predictive machine learning model. We showcase the robustness of the INSRTR strategy on proteins with diverse folds and biological functions, including enzymes, signaling mediators, DNA binders, transcriptional regulators, reporters, and antibody domains implemented as chimeric antigen receptors in T cells. Our findings highlight the potential of INSRTR as a powerful tool for precise control of protein function, advancing our understanding of biological processes and developing biotechnological and therapeutic interventions.
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Affiliation(s)
- Tjaša Plaper
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Estera Merljak
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Tina Fink
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Tadej Satler
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
- Interdisciplinary doctoral study of biomedicine, Medical Faculty, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Ajasja Ljubetič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Duško Lainšček
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Vid Jazbec
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
- Interdisciplinary doctoral study of biomedicine, Medical Faculty, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
- Centre for Technologies of Gene and Cell Therapy, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Sintija Stevanoska
- Department of knowledge technologies, Jožef Stefan Institute, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Sašo Džeroski
- Department of knowledge technologies, Jožef Stefan Institute, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia.
- Centre for Technologies of Gene and Cell Therapy, Hajdrihova 19, SI-1000, Ljubljana, Slovenia.
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6
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Rihtar E, Fink T, Jerala R. Coiled-Coil Interaction Toolbox for Engineering Mammalian Cells. Methods Mol Biol 2024; 2774:31-41. [PMID: 38441756 DOI: 10.1007/978-1-0716-3718-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Protein interactions play a crucial role in a variety of biological processes. Therefore, regulation of these interactions has received considerable attention in terms of synthetic biology tool development. Of those, a toolbox of small peptides known as coiled coils (CCs) represents a unique effective tool for mediating protein-protein interactions because their binding specificity and affinity can be designed and controlled. CC peptides have been used as a building module for designing synthetic regulatory circuits in mammalian cells, construction of fast response to a signal, amplification of the response, and localization and regulation of function of diverse proteins. In this chapter, we describe a designed set of CCs used for mammalian cell engineering and provide a protocol for the construction of CC-mediated logic circuits in mammalian cells. Ultimately, these tools could be used for diverse biotechnological and therapeutic applications.
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Affiliation(s)
- Erik Rihtar
- National Institute of Chemistry, Department of Synthetic Biology and Immunology, Ljubljana, Slovenia
| | - Tina Fink
- National Institute of Chemistry, Department of Synthetic Biology and Immunology, Ljubljana, Slovenia
| | - Roman Jerala
- National Institute of Chemistry, Department of Synthetic Biology and Immunology, Ljubljana, Slovenia.
- EN-FIST Centre of Excellence, Ljubljana, Slovenia.
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7
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Ramšak M, Ramirez DA, Hough LE, Shirts MR, Vidmar S, Eleršič Filipič K, Anderluh G, Jerala R. Programmable de novo designed coiled coil-mediated phase separation in mammalian cells. Nat Commun 2023; 14:7973. [PMID: 38042897 PMCID: PMC10693550 DOI: 10.1038/s41467-023-43742-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/17/2023] [Indexed: 12/04/2023] Open
Abstract
Membraneless liquid compartments based on phase-separating biopolymers have been observed in diverse cell types and attributed to weak multivalent interactions predominantly based on intrinsically disordered domains. The design of liquid-liquid phase separated (LLPS) condensates based on de novo designed tunable modules that interact in a well-understood, controllable manner could improve our understanding of this phenomenon and enable the introduction of new features. Here we report the construction of CC-LLPS in mammalian cells, based on designed coiled-coil (CC) dimer-forming modules, where the stability of CC pairs, their number, linkers, and sequential arrangement govern the transition between diffuse, liquid and immobile condensates and are corroborated by coarse-grained molecular simulations. Through modular design, we achieve multiple coexisting condensates, chemical regulation of LLPS, condensate fusion, formation from either one or two polypeptide components or LLPS regulation by a third polypeptide chain. These findings provide further insights into the principles underlying LLPS formation and a design platform for controlling biological processes.
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Affiliation(s)
- Maruša Ramšak
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Interdisciplinary doctoral study of biomedicine, Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Dominique A Ramirez
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Loren E Hough
- Department of Physics and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Sara Vidmar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Interdisciplinary doctoral study of biomedicine, Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Kristina Eleršič Filipič
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.
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8
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Makri Pistikou AM, Cremers GAO, Nathalia BL, Meuleman TJ, Bögels BWA, Eijkens BV, de Dreu A, Bezembinder MTH, Stassen OMJA, Bouten CCV, Merkx M, Jerala R, de Greef TFA. Engineering a scalable and orthogonal platform for synthetic communication in mammalian cells. Nat Commun 2023; 14:7001. [PMID: 37919273 PMCID: PMC10622552 DOI: 10.1038/s41467-023-42810-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 10/23/2023] [Indexed: 11/04/2023] Open
Abstract
The rational design and implementation of synthetic mammalian communication systems can unravel fundamental design principles of cell communication circuits and offer a framework for engineering of designer cell consortia with potential applications in cell therapeutics. Here, we develop the foundations of an orthogonal, and scalable mammalian synthetic communication platform that exploits the programmability of synthetic receptors and selective affinity and tunability of diffusing coiled-coil peptides. Leveraging the ability of coiled-coils to exclusively bind to a cognate receptor, we demonstrate orthogonal receptor activation and Boolean logic operations at the receptor level. We show intercellular communication based on synthetic receptors and secreted multidomain coiled-coils and demonstrate a three-cell population system that can perform AND gate logic. Finally, we show CC-GEMS receptor-dependent therapeutic protein expression. Our work provides a modular and scalable framework for the engineering of complex cell consortia, with the potential to expand the aptitude of cell therapeutics and diagnostics.
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Affiliation(s)
- Anna-Maria Makri Pistikou
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Glenn A O Cremers
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Bryan L Nathalia
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Theodorus J Meuleman
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Utrecht, The Netherlands
| | - Bas W A Bögels
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Bruno V Eijkens
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Anne de Dreu
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Maarten T H Bezembinder
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Oscar M J A Stassen
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Carlijn C V Bouten
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Tom F A de Greef
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Utrecht, The Netherlands.
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
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9
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Jovičić EJ, Janež AP, Eichmann TO, Koren Š, Brglez V, Jordan PM, Gerstmeier J, Lainšček D, Golob-Urbanc A, Jerala R, Lambeau G, Werz O, Zimmermann R, Petan T. Lipid droplets control mitogenic lipid mediator production in human cancer cells. Mol Metab 2023; 76:101791. [PMID: 37586657 PMCID: PMC10470291 DOI: 10.1016/j.molmet.2023.101791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/29/2023] [Accepted: 08/08/2023] [Indexed: 08/18/2023] Open
Abstract
OBJECTIVES Polyunsaturated fatty acids (PUFAs) are structural components of membrane phospholipids and precursors of oxygenated lipid mediators with diverse functions, including the control of cell growth, inflammation and tumourigenesis. However, the molecular pathways that control the availability of PUFAs for lipid mediator production are not well understood. Here, we investigated the crosstalk of three pathways in the provision of PUFAs for lipid mediator production: (i) secreted group X phospholipase A2 (GX sPLA2) and (ii) cytosolic group IVA PLA2 (cPLA2α), both mobilizing PUFAs from membrane phospholipids, and (iii) adipose triglyceride lipase (ATGL), which mediates the degradation of triacylglycerols (TAGs) stored in cytosolic lipid droplets (LDs). METHODS We combined lipidomic and functional analyses in cancer cell line models to dissect the trafficking of PUFAs between membrane phospholipids and LDs and determine the role of these pathways in lipid mediator production, cancer cell proliferation and tumour growth in vivo. RESULTS We demonstrate that lipid mediator production strongly depends on TAG turnover. GX sPLA2 directs ω-3 and ω-6 PUFAs from membrane phospholipids into TAG stores, whereas ATGL is required for their entry into lipid mediator biosynthetic pathways. ATGL controls the release of PUFAs from LD stores and their conversion into cyclooxygenase- and lipoxygenase-derived lipid mediators under conditions of nutrient sufficiency and during serum starvation. In starving cells, ATGL also promotes the incorporation of LD-derived PUFAs into phospholipids, representing substrates for cPLA2α. Furthermore, we demonstrate that the built-up of TAG stores by acyl-CoA:diacylglycerol acyltransferase 1 (DGAT1) is required for the production of mitogenic lipid signals that promote cancer cell proliferation and tumour growth. CONCLUSION This study shifts the paradigm of PLA2-driven lipid mediator signalling and identifies LDs as central lipid mediator production hubs. Targeting DGAT1-mediated LD biogenesis is a promising strategy to restrict lipid mediator production and tumour growth.
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Affiliation(s)
- Eva Jarc Jovičić
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Anja Pucer Janež
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Thomas O Eichmann
- Institute of Molecular Biosciences, University of Graz, Graz, Austria; Center for Explorative Lipidomics, BioTechMed-Graz, Graz, Austria
| | - Špela Koren
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Vesna Brglez
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Paul M Jordan
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University Jena, Jena, Germany
| | - Jana Gerstmeier
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University Jena, Jena, Germany
| | - Duško Lainšček
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia; EN-FIST, Centre of Excellence, Ljubljana, Slovenia
| | - Anja Golob-Urbanc
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia; EN-FIST, Centre of Excellence, Ljubljana, Slovenia
| | - Gérard Lambeau
- Université Côte d'Azur (UCA), Centre National de la Recherche Scientifique (CNRS), Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), UMR7275, Valbonne Sophia Antipolis, France
| | - Oliver Werz
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University Jena, Jena, Germany
| | - Robert Zimmermann
- Institute of Molecular Biosciences, University of Graz, Graz, Austria; BioTechMed-Graz, University of Graz, Graz, Austria
| | - Toni Petan
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia.
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10
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Satler T, Hadži S, Jerala R. Crystal Structure of de Novo Designed Coiled-Coil Protein Origami Triangle. J Am Chem Soc 2023; 145:16995-17000. [PMID: 37486611 PMCID: PMC10416210 DOI: 10.1021/jacs.3c05531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Indexed: 07/25/2023]
Abstract
Coiled-coil protein origami (CCPO) uses modular coiled-coil building blocks and topological principles to design polyhedral structures distinct from those of natural globular proteins. While the CCPO strategy has proven successful in designing diverse protein topologies, no high-resolution structural information has been available about these novel protein folds. Here we report the crystal structure of a single-chain CCPO in the shape of a triangle. While neither cyclization nor the addition of nanobodies enabled crystallization, it was ultimately facilitated by the inclusion of a GCN2 homodimer. Triangle edges are formed by the orthogonal parallel coiled-coil dimers P1:P2, P3:P4, and GCN2 connected by short linkers. A triangle has a large central cavity and is additionally stabilized by side-chain interactions between neighboring segments at each vertex. The crystal lattice is densely packed and stabilized by a large number of contacts between triangles. Interestingly, the polypeptide chain folds into a trefoil-type protein knot topology, and AlphaFold2 fails to predict the correct fold. The structure validates the modular CC-based protein design strategy, providing molecular insight underlying CCPO stabilization and new opportunities for the design.
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Affiliation(s)
- Tadej Satler
- Department
of Synthetic Biology and Immunology, National
Institute of Chemistry, 1000 Ljubljana, Slovenia
- Interdisciplinary
Doctoral Programme in Biomedicine, University
of Ljubljana, 1000 Ljubljana, Slovenia
| | - San Hadži
- Department
of Synthetic Biology and Immunology, National
Institute of Chemistry, 1000 Ljubljana, Slovenia
- Department
of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Roman Jerala
- Department
of Synthetic Biology and Immunology, National
Institute of Chemistry, 1000 Ljubljana, Slovenia
- EN-FIST
Centre of Excellence, 1000 Ljubljana, Slovenia
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11
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Boldridge WC, Ljubetič A, Kim H, Lubock N, Szilágyi D, Lee J, Brodnik A, Jerala R, Kosuri S. A multiplexed bacterial two-hybrid for rapid characterization of protein-protein interactions and iterative protein design. Nat Commun 2023; 14:4636. [PMID: 37532706 PMCID: PMC10397247 DOI: 10.1038/s41467-023-38697-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/11/2023] [Indexed: 08/04/2023] Open
Abstract
Protein-protein interactions (PPIs) are crucial for biological functions and have applications ranging from drug design to synthetic cell circuits. Coiled-coils have been used as a model to study the sequence determinants of specificity. However, building well-behaved sets of orthogonal pairs of coiled-coils remains challenging due to inaccurate predictions of orthogonality and difficulties in testing at scale. To address this, we develop the next-generation bacterial two-hybrid (NGB2H) method, which allows for the rapid exploration of interactions of programmed protein libraries in a quantitative and scalable way using next-generation sequencing readout. We design, build, and test large sets of orthogonal synthetic coiled-coils, assayed over 8,000 PPIs, and used the dataset to train a more accurate coiled-coil scoring algorithm (iCipa). After characterizing nearly 18,000 new PPIs, we identify to the best of our knowledge the largest set of orthogonal coiled-coils to date, with fifteen on-target interactions. Our approach provides a powerful tool for the design of orthogonal PPIs.
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Affiliation(s)
- W Clifford Boldridge
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Ajasja Ljubetič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000, Ljubljana, Slovenia.
- EN-FIST Centre of Excellence, 1000, Ljubljana, Slovenia.
| | - Hwangbeom Kim
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
- Samsung Biologics, Incheon, Republic of Korea
| | - Nathan Lubock
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
- Octant Inc, Emeryville, CA, 94608, USA
| | | | - Jonathan Lee
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, 90095, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | | | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000, Ljubljana, Slovenia.
- EN-FIST Centre of Excellence, 1000, Ljubljana, Slovenia.
| | - Sriram Kosuri
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA.
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Octant Inc, Emeryville, CA, 94608, USA.
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12
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Lainšček D, Golob-Urbanc A, Mikolič V, Pantović-Žalig J, Malenšek Š, Jerala R. Regulation of CD19 CAR-T cell activation based on an engineered downstream transcription factor. Mol Ther Oncolytics 2023; 29:77-90. [PMID: 37223115 PMCID: PMC10200817 DOI: 10.1016/j.omto.2023.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/24/2023] [Indexed: 05/25/2023] Open
Abstract
CAR-T cells present a highly effective therapeutic option for several malignant diseases, based on their ability to recognize the selected tumor surface marker in an MHC-independent manner. This triggers cell activation and cytokine production, resulting in the killing of the cancerous cell presenting markers recognized by the chimeric antigen receptor. CAR-T cells are highly potent serial killers that may cause serious side effects, so their activity needs to be carefully controlled. Here we designed a system to control the proliferation and activation state of CARs based on downstream NFAT transcription factors, whose activity can be regulated via chemically induced heterodimerization systems. Chemical regulators were used to either transiently trigger engineered T cell proliferation or suppress CAR-mediated activation when desired or to enhance activation of CAR-T cells upon engagement of cancer cells, shown also in vivo. Additionally, an efficient sensor to monitor activated CD19 CAR-T cells in vivo was introduced. This implementation in CAR-T cell regulation offers an efficient way for on-demand external control of CAR-T cell activity to improve their safety.
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Affiliation(s)
- Duško Lainšček
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia
- EN-FIST Centre of Excellence, Trg Osvobodilne fronte 13, Ljubljana 1000, Slovenia
| | - Anja Golob-Urbanc
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia
| | - Veronika Mikolič
- Department of Hematology, Division of Internal Medicine, University Medical Center Ljubljana, Zaloška 7, Ljubljana 1000, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Jelica Pantović-Žalig
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Špela Malenšek
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia
- EN-FIST Centre of Excellence, Trg Osvobodilne fronte 13, Ljubljana 1000, Slovenia
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13
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Kadunc Polajnar L, Lainšček D, Gašperšič R, Sušjan-Leite P, Kovačič U, Butinar M, Turk B, Jerala R, Hafner-Bratkovič I. Engineered combinatorial cell device for wound healing and bone regeneration. Front Bioeng Biotechnol 2023; 11:1168330. [PMID: 37234478 PMCID: PMC10206319 DOI: 10.3389/fbioe.2023.1168330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Growth factors are the key regulators that promote tissue regeneration and healing processes. While the effects of individual growth factors are well documented, a combination of multiple secreted growth factors underlies stem cell-mediated regeneration. To avoid the potential dangers and labor-intensive individual approach of stem cell therapy while maintaining their regeneration-promoting effects based on multiple secreted growth factors, we engineered a "mix-and-match" combinatorial platform based on a library of cell lines producing growth factors. Treatment with a combination of growth factors secreted by engineered mammalian cells was more efficient than with individual growth factors or even stem cell-conditioned medium in a gap closure assay. Furthermore, we implemented in a mouse model a device for allogenic cell therapy for an in situ production of growth factors, where it improved cutaneous wound healing. Augmented bone regeneration was achieved on calvarial bone defects in rats treated with a cell device secreting IGF, FGF, PDGF, TGF-β, and VEGF. In both in vivo models, the systemic concentration of secreted factors was negligible, demonstrating the local effect of the regeneration device. Finally, we introduced a genetic switch that enables temporal control over combinations of trophic factors released at different stages of regeneration mimicking the maturation of natural wound healing to improve therapy and prevent scar formation.
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Affiliation(s)
- Lucija Kadunc Polajnar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Duško Lainšček
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Rok Gašperšič
- Department of Oral Medicine and Periodontology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Petra Sušjan-Leite
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Uroš Kovačič
- Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Miha Butinar
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Ljubljana, Slovenia
| | - Boris Turk
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Iva Hafner-Bratkovič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Ljubljana, Slovenia
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14
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Merljak E, Malovrh B, Jerala R. Segmentation strategy of de novo designed four-helical bundles expands protein oligomerization modalities for cell regulation. Nat Commun 2023; 14:1995. [PMID: 37031229 PMCID: PMC10082849 DOI: 10.1038/s41467-023-37765-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/30/2023] [Indexed: 04/10/2023] Open
Abstract
Protein-protein interactions govern most biological processes. New protein assemblies can be introduced through the fusion of selected proteins with di/oligomerization domains, which interact specifically with their partners but not with other cellular proteins. While four-helical bundle proteins (4HB) have typically been assembled from two segments, each comprising two helices, here we show that they can be efficiently segmented in various ways, expanding the number of combinations generated from a single 4HB. We implement a segmentation strategy of 4HB to design two-, three-, or four-chain combinations for the recruitment of multiple protein components. Different segmentations provide new insight into the role of individual helices for 4HB assembly. We evaluate 4HB segmentations for potential use in mammalian cells for the reconstitution of a protein reporter, transcriptional activation, and inducible 4HB assembly. Furthermore, the implementation of trimerization is demonstrated as a modular chimeric antigen receptor for the recognition of multiple cancer antigens.
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Affiliation(s)
- Estera Merljak
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Interdisciplinary Doctoral Programme of Biomedicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Benjamin Malovrh
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.
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15
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Strmšek Ž, Snoj J, Satler T, Jerala R. Coiled-Coil Protein Origami: Design, Isolation, and Characterization. Methods Mol Biol 2023; 2671:3-48. [PMID: 37308636 DOI: 10.1007/978-1-0716-3222-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Coiled-coil protein origami (CCPO) is a rationally designed de novo protein fold, constructed by concatenating coiled-coil forming segments into a polypeptide chain, that folds into polyhedral nano-cages. To date, nanocages in the shape of a tetrahedron, square pyramid, trigonal prism, and trigonal bipyramid have been successfully designed and extensively characterized following the design principles of CCPO. These designed protein scaffolds and their favorable biophysical properties are suitable for functionalization and other various biotechnological applications. To further facilitate the development, we are presenting a detailed guide to the world of CCPO, starting from design (CoCoPOD, an integrated platform for designing CCPO strictures) and cloning (modified Golden-gate assembly) to fermentation and isolation (NiNTA, Strep-trap, IEX, and SEC) concluding with standard characterization techniques (CD, SEC-MALS, and SAXS).
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Affiliation(s)
- Žiga Strmšek
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Jaka Snoj
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Tadej Satler
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.
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16
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Abstract
Regulation of epigenomic functions requires controlled site-specific alteration of epigenetic information. This can be achieved by using designed DNA-binding domains, associated with effector domains, that function as targeted transcription factors or epigenetic modifiers. These effectors have been employed to study the implications of epigenetic modifications, and sequence-specific targeting has been instrumental in understanding the effect of these modification on gene regulation. Ultimately, these tools could be used for therapeutic applications to revert the epigenetic aberrations that have been linked to various diseases. The ability to spatiotemporally control gene expression is especially important for precise regulation of the epigenomic state. In this chapter, we describe the protocol for achieving highly efficient small molecule-inducible transcriptional activation of endogenous mammalian genes, mediated by a dCas9-based system that recruits transcriptional activation domains binding to a chain of concatenated coiled-coil peptides.
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Affiliation(s)
- Tina Lebar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.
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17
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Jazbec V, Jerala R, Benčina M. Proteolytically Activated CRAC Effectors through Designed Intramolecular Inhibition. ACS Synth Biol 2022; 11:2756-2765. [PMID: 35802180 PMCID: PMC9396659 DOI: 10.1021/acssynbio.2c00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Highly regulated intracellular calcium entry affects
numerous cellular
physiological events. External regulation of intracellular calcium
signaling presents a great opportunity for the artificial regulation
of cellular activity. Calcium entry can be mediated by STIM proteins
interacting with Orai calcium channels; therefore, the STIM1–Orai1
pair has become a tool for artificially modulating calcium entry.
We report on an innovative genetically engineered protease-activated
Orai activator called PACE. CAD self-dimerization and activation were
inhibited with a coiled-coil forming peptide pair linked to CAD via
a protease cleavage site. PACE generated sustained calcium entry after
its activation with a reconstituted split protease. We also generated
PACE, whose transcriptional activation of NFAT was triggered by PPV
or TEV protease. Using PACE, we successfully activated the native
NFAT signaling pathway and the production of cytokines in a T-cell
line. PACE represents a useful tool for generating sustained calcium
entry to initiate calcium-dependent protein translation. PACE provides
a promising template for the construction of links between various
protease activation pathways and calcium signaling.
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Affiliation(s)
- Vid Jazbec
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.,Interfaculty Doctoral Study of Biomedicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Trg Osvobodilne fronte 13, SI-1000 Ljubljana, Slovenia
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Trg Osvobodilne fronte 13, SI-1000 Ljubljana, Slovenia
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18
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Lainšček D, Forstnerič V, Mikolič V, Malenšek Š, Pečan P, Benčina M, Sever M, Podgornik H, Jerala R. Coiled-coil heterodimer-based recruitment of an exonuclease to CRISPR/Cas for enhanced gene editing. Nat Commun 2022; 13:3604. [PMID: 35739111 PMCID: PMC9226073 DOI: 10.1038/s41467-022-31386-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 06/16/2022] [Indexed: 11/16/2022] Open
Abstract
The CRISPR/Cas system has emerged as a powerful and versatile genome engineering tool, revolutionizing biological and biomedical sciences, where an improvement of efficiency could have a strong impact. Here we present a strategy to enhance gene editing based on the concerted action of Cas9 and an exonuclease. Non-covalent recruitment of exonuclease to Cas9/gRNA complex via genetically encoded coiled-coil based domains, termed CCExo, recruited the exonuclease to the cleavage site and robustly increased gene knock-out due to progressive DNA strand recession at the cleavage site, causing decreased re-ligation of the nonedited DNA. CCExo exhibited increased deletion size and enhanced gene inactivation efficiency in the context of several DNA targets, gRNA selection, Cas variants, tested cell lines and type of delivery. Targeting a sequence-specific oncogenic chromosomal translocation using CCExo in cells of chronic myelogenous leukemia patients and in an animal model led to the reduction or elimination of cancer, establishing it as a highly specific tool for treating CML and potentially other appropriate diseases with genetic etiology.
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Affiliation(s)
- Duško Lainšček
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana, 1000, Slovenia
- EN-FIST Centre of Excellence, Trg Osvobodilne fronte 13, Ljubljana, 1000, Slovenia
| | - Vida Forstnerič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana, 1000, Slovenia
| | - Veronika Mikolič
- Department of Hematology, Division of Internal Medicine, University Medical Centre Ljubljana, Zaloška 7, Ljubljana, 1000, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, Ljubljana, 1000, Slovenia
| | - Špela Malenšek
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana, 1000, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, Ljubljana, 1000, Slovenia
| | - Peter Pečan
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana, 1000, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, Ljubljana, 1000, Slovenia
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana, 1000, Slovenia
- EN-FIST Centre of Excellence, Trg Osvobodilne fronte 13, Ljubljana, 1000, Slovenia
| | - Matjaž Sever
- Department of Hematology, Division of Internal Medicine, University Medical Centre Ljubljana, Zaloška 7, Ljubljana, 1000, Slovenia
- Faculty of Medicine, University of Ljubljana, Korytkova 2, Ljubljana, 1000, Slovenia
| | - Helena Podgornik
- Department of Hematology, Division of Internal Medicine, University Medical Centre Ljubljana, Zaloška 7, Ljubljana, 1000, Slovenia
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana, 1000, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana, 1000, Slovenia.
- EN-FIST Centre of Excellence, Trg Osvobodilne fronte 13, Ljubljana, 1000, Slovenia.
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19
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Aupič J, Lapenta F, Strmšek Ž, Merljak E, Plaper T, Jerala R. Metal ion-regulated assembly of designed modular protein cages. Sci Adv 2022; 8:eabm8243. [PMID: 35714197 PMCID: PMC9205593 DOI: 10.1126/sciadv.abm8243] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
Coiled-coil (CC) dimers are versatile, customizable building modules for the design of diverse protein architectures unknown in nature. Incorporation of dynamic self-assembly, regulated by a selected chemical signal, represents an important challenge in the construction of functional polypeptide nanostructures. Here, we engineered metal binding sites to render an orthogonal set of CC heterodimers Zn(II)-responsive as a generally applicable principle. The designed peptides assemble into CC heterodimers only in the presence of Zn(II) ions, reversibly dissociate by metal ion sequestration, and additionally act as pH switches, with low pH triggering disassembly. The developed Zn(II)-responsive CC set is used to construct programmable folding of CC-based nanostructures, from protein triangles to a two-chain bipyramidal protein cage that closes and opens depending on the metal ion. This demonstrates that dynamic self-assembly can be designed into CC-based protein cages by incorporation of metal ion-responsive CC building modules that act as conformational switches and that could also be used in other contexts.
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Affiliation(s)
- Jana Aupič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Fabio Lapenta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia
| | - Žiga Strmšek
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Estera Merljak
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- Interdisciplinary Doctoral Programme in Biomedicine, University of Ljubljana, Kongresni trg 12, SI-1000 Ljubljana, Slovenia
| | - Tjaša Plaper
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- Interdisciplinary Doctoral Programme in Biomedicine, University of Ljubljana, Kongresni trg 12, SI-1000 Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia
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20
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Leben K, Strmšek Ž, Lebar T, Verbič A, Dragovan M, Omersa N, Anderluh G, Jerala R. Binding of the transcription activator-like effector augments transcriptional regulation by another transcription factor. Nucleic Acids Res 2022; 50:6562-6574. [PMID: 35670660 PMCID: PMC9226504 DOI: 10.1093/nar/gkac454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/02/2022] [Indexed: 01/27/2023] Open
Abstract
DNA transcription is regulated by a range of diverse mechanisms and primarily by transcription factors that recruit the RNA polymerase complex to the promoter region on the DNA. Protein binding to DNA at nearby or distant sites can synergistically affect this process in a variety of ways, but mainly through direct interactions between DNA-binding proteins. Here we show that a Transcription Activator-Like Effector (TALE), which lacks an activation domain, can enhance transcription in mammalian cells when it binds in the vicinity of and without direct interaction with several different dimeric or monomeric transcription factors. This effect was observed for several TALEs regardless of the recognition sequences and their DNA-bound orientation. TALEs can exert an effect over the distance of tens of nucleotides and it also potentiated KRAB-mediated repression. The augmentation of transcriptional regulation of another transcription factor is characteristic of TALEs, as it was not observed for dCas9/gRNA, zinc finger, or Gal4 DNA-binding domains. We propose that this mechanism involves an allosteric effect exerted on DNA structure or dynamics. This mechanism could be used to modulate transcription but may also play a role in the natural context of TALEs.
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Affiliation(s)
- Katja Leben
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,Interdisciplinary Doctoral Programme in Biomedicine, University of Ljubljana, Kongresni trg 12, SI-1000 Ljubljana, Slovenia
| | - Žiga Strmšek
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Tina Lebar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Anže Verbič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,Interdisciplinary Doctoral Programme in Biomedicine, University of Ljubljana, Kongresni trg 12, SI-1000 Ljubljana, Slovenia
| | - Matej Dragovan
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Neža Omersa
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
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21
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Fink T, Jerala R. Designed protease-based signaling networks. Curr Opin Chem Biol 2022; 68:102146. [DOI: 10.1016/j.cbpa.2022.102146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/09/2022] [Accepted: 03/14/2022] [Indexed: 12/27/2022]
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22
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Avbelj M, Hafner-Bratkovič I, Lainšček D, Manček-Keber M, Peternelj TT, Panter G, Treon SP, Gole B, Potočnik U, Jerala R. Cleavage-Mediated Regulation of Myd88 Signaling by Inflammasome-Activated Caspase-1. Front Immunol 2022; 12:790258. [PMID: 35069570 PMCID: PMC8767097 DOI: 10.3389/fimmu.2021.790258] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/15/2021] [Indexed: 01/07/2023] Open
Abstract
Coordination among multiple signaling pathways ensures an appropriate immune response, where a signaling pathway may impair or augment another signaling pathway. Here, we report a negative feedback regulation of signaling through the key innate immune mediator MyD88 by inflammasome-activated caspase-1. NLRP3 inflammasome activation impaired agonist- or infection-induced TLR signaling and cytokine production through the proteolytic cleavage of MyD88 by caspase-1. Site-specific mutagenesis was used to identify caspase-1 cleavage site within MyD88 intermediary segment. Different cleavage site location within MyD88 defined the functional consequences of MyD88 cleavage between mouse and human cells. LPS/monosodium urate–induced mouse inflammation model corroborated the physiological role of this mechanism of regulation, that could be reversed by chemical inhibition of NLRP3. While Toll/interleukin-1 receptor (TIR) domain released by MyD88 cleavage additionally contributed to the inhibition of signaling, Waldenström’s macroglobulinemia associated MyD88L265P mutation is able to evade the caspase-1-mediated inhibition of MyD88 signaling through the ability of its TIRL265P domain to recruit full length MyD88 and facilitate signaling. The characterization of this mechanism reveals an additional layer of innate immunity regulation.
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Affiliation(s)
- Monika Avbelj
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Iva Hafner-Bratkovič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Duško Lainšček
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Mateja Manček-Keber
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Tina Tinkara Peternelj
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Gabriela Panter
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Steven P Treon
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, United States
| | - Boris Gole
- Centre for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Uroš Potočnik
- Centre for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia.,Laboratory of Biochemistry, Molecular Biology and Genomics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Ljubljana, Slovenia
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23
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Rajh E, Šket T, Praznik A, Sušjan P, Šmid A, Urbančič D, Mlinarič-Raščan I, Kogovšek P, Demšar T, Milavec M, Prosenc Trilar K, Jensterle Ž, Zidarn M, Tomič V, Turel G, Lejko-Zupanc T, Jerala R, Benčina M. Robust Saliva-Based RNA Extraction-Free One-Step Nucleic Acid Amplification Test for Mass SARS-CoV-2 Monitoring. Molecules 2021; 26:6617. [PMID: 34771026 PMCID: PMC8588466 DOI: 10.3390/molecules26216617] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 01/19/2023] Open
Abstract
Early diagnosis with rapid detection of the virus plays a key role in preventing the spread of infection and in treating patients effectively. In order to address the need for a straightforward detection of SARS-CoV-2 infection and assessment of viral spread, we developed rapid, sensitive, extraction-free one-step reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP) tests for detecting SARS-CoV-2 in saliva. We analyzed over 700 matched pairs of saliva and nasopharyngeal swab (NSB) specimens from asymptomatic and symptomatic individuals. Saliva, as either an oral cavity swab or passive drool, was collected in an RNA stabilization buffer. The stabilized saliva specimens were heat-treated and directly analyzed without RNA extraction. The diagnostic sensitivity of saliva-based RT-qPCR was at least 95% in individuals with subclinical infection and outperformed RT-LAMP, which had at least 70% sensitivity when compared to NSBs analyzed with a clinical RT-qPCR test. The diagnostic sensitivity for passive drool saliva was higher than that of oral cavity swab specimens (95% and 87%, respectively). A rapid, sensitive one-step extraction-free RT-qPCR test for detecting SARS-CoV-2 in passive drool saliva is operationally simple and can be easily implemented using existing testing sites, thus allowing high-throughput, rapid, and repeated testing of large populations. Furthermore, saliva testing is adequate to detect individuals in an asymptomatic screening program and can help improve voluntary screening compliance for those individuals averse to various forms of nasal collections.
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Affiliation(s)
- Eva Rajh
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, SI-1001 Ljubljana, Slovenia; (E.R.); (T.Š.); (A.P.); (P.S.); (R.J.)
| | - Tina Šket
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, SI-1001 Ljubljana, Slovenia; (E.R.); (T.Š.); (A.P.); (P.S.); (R.J.)
| | - Arne Praznik
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, SI-1001 Ljubljana, Slovenia; (E.R.); (T.Š.); (A.P.); (P.S.); (R.J.)
| | - Petra Sušjan
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, SI-1001 Ljubljana, Slovenia; (E.R.); (T.Š.); (A.P.); (P.S.); (R.J.)
| | - Alenka Šmid
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (A.Š.); (D.U.); (I.M.-R.)
| | - Dunja Urbančič
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (A.Š.); (D.U.); (I.M.-R.)
| | - Irena Mlinarič-Raščan
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (A.Š.); (D.U.); (I.M.-R.)
| | - Polona Kogovšek
- Department of Biotechnology and Systems Biology, National Institute of Biology, SI-1000 Ljubljana, Slovenia; (P.K.); (T.D.); (M.M.)
| | - Tina Demšar
- Department of Biotechnology and Systems Biology, National Institute of Biology, SI-1000 Ljubljana, Slovenia; (P.K.); (T.D.); (M.M.)
| | - Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology, SI-1000 Ljubljana, Slovenia; (P.K.); (T.D.); (M.M.)
| | - Katarina Prosenc Trilar
- National Laboratory of Health, Environment, and Food, Laboratory for Public Health Virology, SI-1000 Ljubljana, Slovenia; (K.P.T.); (Ž.J.)
| | - Žiga Jensterle
- National Laboratory of Health, Environment, and Food, Laboratory for Public Health Virology, SI-1000 Ljubljana, Slovenia; (K.P.T.); (Ž.J.)
| | - Mihaela Zidarn
- Emergency Service, Health Centre Jesenice, SI-4270 Jesenice, Slovenia;
| | - Viktorija Tomič
- University Clinic of Respiratory and Allergic Diseases, SI-4204 Golnik, Slovenia;
| | - Gabriele Turel
- Department for Infectious Diseases, University Medical Center Ljubljana, SI-1000 Ljubljana, Slovenia; (G.T.); (T.L.-Z.)
| | - Tatjana Lejko-Zupanc
- Department for Infectious Diseases, University Medical Center Ljubljana, SI-1000 Ljubljana, Slovenia; (G.T.); (T.L.-Z.)
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, SI-1001 Ljubljana, Slovenia; (E.R.); (T.Š.); (A.P.); (P.S.); (R.J.)
- EN-FIST Centre of Excellence, SI-1000 Ljubljana, Slovenia
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, SI-1001 Ljubljana, Slovenia; (E.R.); (T.Š.); (A.P.); (P.S.); (R.J.)
- EN-FIST Centre of Excellence, SI-1000 Ljubljana, Slovenia
- Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia
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24
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Manček-Keber M, Hafner-Bratkovič I, Lainšček D, Benčina M, Govednik T, Orehek S, Plaper T, Jazbec V, Bergant V, Grass V, Pichlmair A, Jerala R. Disruption of disulfides within RBD of SARS-CoV-2 spike protein prevents fusion and represents a target for viral entry inhibition by registered drugs. FASEB J 2021; 35:e21651. [PMID: 34004056 PMCID: PMC8206760 DOI: 10.1096/fj.202100560r] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/11/2022]
Abstract
The SARS‐CoV‐2 pandemic imposed a large burden on health and society. Therapeutics targeting different components and processes of the viral infection replication cycle are being investigated, particularly to repurpose already approved drugs. Spike protein is an important target for both vaccines and therapeutics. Insights into the mechanisms of spike‐ACE2 binding and cell fusion could support the identification of compounds with inhibitory effects. Here, we demonstrate that the integrity of disulfide bonds within the receptor‐binding domain (RBD) plays an important role in the membrane fusion process although their disruption does not prevent binding of spike protein to ACE2. Several reducing agents and thiol‐reactive compounds are able to inhibit viral entry. N‐acetyl cysteine amide, L‐ascorbic acid, JTT‐705, and auranofin prevented syncytia formation, viral entry into cells, and infection in a mouse model, supporting disulfides of the RBD as a therapeutically relevant target.
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Affiliation(s)
- Mateja Manček-Keber
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,Centre of Excellence EN-FIST, Ljubljana, Slovenia
| | - Iva Hafner-Bratkovič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,Centre of Excellence EN-FIST, Ljubljana, Slovenia
| | - Duško Lainšček
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,Centre of Excellence EN-FIST, Ljubljana, Slovenia
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,Centre of Excellence EN-FIST, Ljubljana, Slovenia
| | - Tea Govednik
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,Graduate School of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Sara Orehek
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,Graduate School of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tjaša Plaper
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,Graduate School of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Vid Jazbec
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,Graduate School of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Valter Bergant
- Immunopathology of Virus Infections Laboratory, Institute of Virology, Technical University of Munich, Munich, Germany
| | - Vincent Grass
- Immunopathology of Virus Infections Laboratory, Institute of Virology, Technical University of Munich, Munich, Germany
| | - Andreas Pichlmair
- Immunopathology of Virus Infections Laboratory, Institute of Virology, Technical University of Munich, Munich, Germany
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,Centre of Excellence EN-FIST, Ljubljana, Slovenia
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25
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Plaper T, Aupič J, Dekleva P, Lapenta F, Keber MM, Jerala R, Benčina M. Coiled-coil heterodimers with increased stability for cellular regulation and sensing SARS-CoV-2 spike protein-mediated cell fusion. Sci Rep 2021; 11:9136. [PMID: 33911109 PMCID: PMC8080620 DOI: 10.1038/s41598-021-88315-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/12/2021] [Indexed: 12/19/2022] Open
Abstract
Coiled-coil (CC) dimer-forming peptides are attractive designable modules for mediating protein association. Highly stable CCs are desired for biological activity regulation and assay. Here, we report the design and versatile applications of orthogonal CC dimer-forming peptides with a dissociation constant in the low nanomolar range. In vitro stability and specificity was confirmed in mammalian cells by enzyme reconstitution, transcriptional activation using a combination of DNA-binding and a transcriptional activation domain, and cellular-enzyme-activity regulation based on externally-added peptides. In addition to cellular regulation, coiled-coil-mediated reporter reconstitution was used for the detection of cell fusion mediated by the interaction between the spike protein of pandemic SARS-CoV2 and the ACE2 receptor. This assay can be used to investigate the mechanism of viral spike protein-mediated fusion or screening for viral inhibitors under biosafety level 1 conditions.
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Affiliation(s)
- Tjaša Plaper
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.,Interfaculty Doctoral Study of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Jana Aupič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia
| | - Petra Dekleva
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia
| | - Fabio Lapenta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, 1000, Ljubljana, Slovenia
| | - Mateja Manček Keber
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, 1000, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia. .,EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, 1000, Ljubljana, Slovenia.
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia. .,EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, 1000, Ljubljana, Slovenia.
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26
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Lainšček D, Fink T, Forstnerič V, Hafner-Bratkovič I, Orehek S, Strmšek Ž, Manček-Keber M, Pečan P, Esih H, Malenšek Š, Aupič J, Dekleva P, Plaper T, Vidmar S, Kadunc L, Benčina M, Omersa N, Anderluh G, Pojer F, Lau K, Hacker D, Correia BE, Peterhoff D, Wagner R, Bergant V, Herrmann A, Pichlmair A, Jerala R. A Nanoscaffolded Spike-RBD Vaccine Provides Protection against SARS-CoV-2 with Minimal Anti-Scaffold Response. Vaccines (Basel) 2021; 9:vaccines9050431. [PMID: 33925446 PMCID: PMC8146944 DOI: 10.3390/vaccines9050431] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/22/2021] [Accepted: 04/25/2021] [Indexed: 02/06/2023] Open
Abstract
The response of the adaptive immune system is augmented by multimeric presentation of a specific antigen, resembling viral particles. Several vaccines have been designed based on natural or designed protein scaffolds, which exhibited a potent adaptive immune response to antigens; however, antibodies are also generated against the scaffold, which may impair subsequent vaccination. In order to compare polypeptide scaffolds of different size and oligomerization state with respect to their efficiency, including anti-scaffold immunity, we compared several strategies of presentation of the RBD domain of the SARS-CoV-2 spike protein, an antigen aiming to generate neutralizing antibodies. A comparison of several genetic fusions of RBD to different nanoscaffolding domains (foldon, ferritin, lumazine synthase, and β-annulus peptide) delivered as DNA plasmids demonstrated a strongly augmented immune response, with high titers of neutralizing antibodies and a robust T-cell response in mice. Antibody titers and virus neutralization were most potently enhanced by fusion to the small β-annulus peptide scaffold, which itself triggered a minimal response in contrast to larger scaffolds. The β-annulus fused RBD protein increased residence in lymph nodes and triggered the most potent viral neutralization in immunization by a recombinant protein. Results of the study support the use of a nanoscaffolding platform using the β-annulus peptide for vaccine design.
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Affiliation(s)
- Duško Lainšček
- EN-FIST, Centre of Excellence, 1000 Ljubljana, Slovenia; (D.L.); (I.H.-B.); (M.M.-K.); (M.B.)
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia; (T.F.); (V.F.); (S.O.); (Ž.S.); (P.P.); (H.E.); (Š.M.); (J.A.); (P.D.); (T.P.); (S.V.); (L.K.)
| | - Tina Fink
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia; (T.F.); (V.F.); (S.O.); (Ž.S.); (P.P.); (H.E.); (Š.M.); (J.A.); (P.D.); (T.P.); (S.V.); (L.K.)
| | - Vida Forstnerič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia; (T.F.); (V.F.); (S.O.); (Ž.S.); (P.P.); (H.E.); (Š.M.); (J.A.); (P.D.); (T.P.); (S.V.); (L.K.)
| | - Iva Hafner-Bratkovič
- EN-FIST, Centre of Excellence, 1000 Ljubljana, Slovenia; (D.L.); (I.H.-B.); (M.M.-K.); (M.B.)
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia; (T.F.); (V.F.); (S.O.); (Ž.S.); (P.P.); (H.E.); (Š.M.); (J.A.); (P.D.); (T.P.); (S.V.); (L.K.)
| | - Sara Orehek
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia; (T.F.); (V.F.); (S.O.); (Ž.S.); (P.P.); (H.E.); (Š.M.); (J.A.); (P.D.); (T.P.); (S.V.); (L.K.)
- Graduate School of Biomedicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Žiga Strmšek
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia; (T.F.); (V.F.); (S.O.); (Ž.S.); (P.P.); (H.E.); (Š.M.); (J.A.); (P.D.); (T.P.); (S.V.); (L.K.)
- Graduate School of Biomedicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Mateja Manček-Keber
- EN-FIST, Centre of Excellence, 1000 Ljubljana, Slovenia; (D.L.); (I.H.-B.); (M.M.-K.); (M.B.)
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia; (T.F.); (V.F.); (S.O.); (Ž.S.); (P.P.); (H.E.); (Š.M.); (J.A.); (P.D.); (T.P.); (S.V.); (L.K.)
| | - Peter Pečan
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia; (T.F.); (V.F.); (S.O.); (Ž.S.); (P.P.); (H.E.); (Š.M.); (J.A.); (P.D.); (T.P.); (S.V.); (L.K.)
- Graduate School of Biomedicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Hana Esih
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia; (T.F.); (V.F.); (S.O.); (Ž.S.); (P.P.); (H.E.); (Š.M.); (J.A.); (P.D.); (T.P.); (S.V.); (L.K.)
- Graduate School of Biomedicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Špela Malenšek
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia; (T.F.); (V.F.); (S.O.); (Ž.S.); (P.P.); (H.E.); (Š.M.); (J.A.); (P.D.); (T.P.); (S.V.); (L.K.)
- Graduate School of Biomedicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Jana Aupič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia; (T.F.); (V.F.); (S.O.); (Ž.S.); (P.P.); (H.E.); (Š.M.); (J.A.); (P.D.); (T.P.); (S.V.); (L.K.)
| | - Petra Dekleva
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia; (T.F.); (V.F.); (S.O.); (Ž.S.); (P.P.); (H.E.); (Š.M.); (J.A.); (P.D.); (T.P.); (S.V.); (L.K.)
- Graduate School of Biomedicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Tjaša Plaper
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia; (T.F.); (V.F.); (S.O.); (Ž.S.); (P.P.); (H.E.); (Š.M.); (J.A.); (P.D.); (T.P.); (S.V.); (L.K.)
- Graduate School of Biomedicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Sara Vidmar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia; (T.F.); (V.F.); (S.O.); (Ž.S.); (P.P.); (H.E.); (Š.M.); (J.A.); (P.D.); (T.P.); (S.V.); (L.K.)
- Graduate School of Biomedicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Lucija Kadunc
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia; (T.F.); (V.F.); (S.O.); (Ž.S.); (P.P.); (H.E.); (Š.M.); (J.A.); (P.D.); (T.P.); (S.V.); (L.K.)
| | - Mojca Benčina
- EN-FIST, Centre of Excellence, 1000 Ljubljana, Slovenia; (D.L.); (I.H.-B.); (M.M.-K.); (M.B.)
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia; (T.F.); (V.F.); (S.O.); (Ž.S.); (P.P.); (H.E.); (Š.M.); (J.A.); (P.D.); (T.P.); (S.V.); (L.K.)
| | - Neža Omersa
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia; (N.O.); (G.A.)
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia; (N.O.); (G.A.)
| | - Florence Pojer
- Protein Production and Structure Core Facility PTPSP- EPFL SV PTECH PTPSP, 1015 Lausanne, Switzerland; (F.P.); (K.L.); (D.H.); (B.E.C.)
| | - Kelvin Lau
- Protein Production and Structure Core Facility PTPSP- EPFL SV PTECH PTPSP, 1015 Lausanne, Switzerland; (F.P.); (K.L.); (D.H.); (B.E.C.)
| | - David Hacker
- Protein Production and Structure Core Facility PTPSP- EPFL SV PTECH PTPSP, 1015 Lausanne, Switzerland; (F.P.); (K.L.); (D.H.); (B.E.C.)
| | - Bruno E. Correia
- Protein Production and Structure Core Facility PTPSP- EPFL SV PTECH PTPSP, 1015 Lausanne, Switzerland; (F.P.); (K.L.); (D.H.); (B.E.C.)
| | - David Peterhoff
- Molecular Microbiology (Virology), Institute of Medical Microbiology and Hygiene, University of Regensburg, 93053 Regensburg, Germany; (D.P.); (R.W.)
| | - Ralf Wagner
- Molecular Microbiology (Virology), Institute of Medical Microbiology and Hygiene, University of Regensburg, 93053 Regensburg, Germany; (D.P.); (R.W.)
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Valter Bergant
- Immunopathology of Virus Infections Laboratory, Institute of Virology, Technical University of Munich, 81675 Munich, Germany; (V.B.); (A.H.); (A.P.)
| | - Alexander Herrmann
- Immunopathology of Virus Infections Laboratory, Institute of Virology, Technical University of Munich, 81675 Munich, Germany; (V.B.); (A.H.); (A.P.)
| | - Andreas Pichlmair
- Immunopathology of Virus Infections Laboratory, Institute of Virology, Technical University of Munich, 81675 Munich, Germany; (V.B.); (A.H.); (A.P.)
- German Center for Infection Research (DZIF), Munich Partner Site, 38124 Braunschweig, Germany
| | - Roman Jerala
- EN-FIST, Centre of Excellence, 1000 Ljubljana, Slovenia; (D.L.); (I.H.-B.); (M.M.-K.); (M.B.)
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia; (T.F.); (V.F.); (S.O.); (Ž.S.); (P.P.); (H.E.); (Š.M.); (J.A.); (P.D.); (T.P.); (S.V.); (L.K.)
- Correspondence:
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27
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Heine H, Adanitsch F, Peternelj TT, Haegman M, Kasper C, Ittig S, Beyaert R, Jerala R, Zamyatina A. Tailored Modulation of Cellular Pro-inflammatory Responses With Disaccharide Lipid A Mimetics. Front Immunol 2021; 12:631797. [PMID: 33815382 PMCID: PMC8012497 DOI: 10.3389/fimmu.2021.631797] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 02/17/2021] [Indexed: 01/08/2023] Open
Abstract
Pro-inflammatory signaling mediated by Toll-like receptor 4 (TLR4)/myeloid differentiation-2 (MD-2) complex plays a crucial role in the instantaneous protection against infectious challenge and largely contributes to recovery from Gram-negative infection. Activation of TLR4 also boosts the adaptive immunity which is implemented in the development of vaccine adjuvants by application of minimally toxic TLR4 activating ligands. The modulation of pro-inflammatory responses via the TLR4 signaling pathway was found beneficial for management of acute and chronic inflammatory disorders including asthma, allergy, arthritis, Alzheimer disease pathology, sepsis, and cancer. The TLR4/MD-2 complex can recognize the terminal motif of Gram-negative bacterial lipopolysaccharide (LPS)—a glycophospholipid lipid A. Although immense progress in understanding the molecular basis of LPS-induced TLR4-mediated signaling has been achieved, gradual, and predictable TLR4 activation by structurally defined ligands has not yet been attained. We report on controllable modulation of cellular pro-inflammatory responses by application of novel synthetic glycolipids—disaccharide-based lipid A mimetics (DLAMs) having picomolar affinity for TLR4/MD-2. Using crystal structure inspired design we have developed endotoxin mimetics where the inherently flexible β(1 → 6)-linked diglucosamine backbone of lipid A is replaced by a conformationally restricted α,α-(1↔1)-linked disaccharide scaffold. The tertiary structure of the disaccharide skeleton of DLAMs mirrors the 3-dimensional shape of TLR4/MD-2 bound E. coli lipid A. Due to exceptional conformational rigidity of the sugar scaffold, the specific 3D organization of DLAM must be preserved upon interaction with proteins. These structural factors along with specific acylation and phosphorylation pattern can ensure picomolar affinity for TLR4 and permit efficient dimerization of TLR4/MD-2/DLAM complexes. Since the binding pose of lipid A in the binding pocket of MD-2 (±180°) is crucial for the expression of biological activity, the chemical structure of DLAMs was designed to permit a predefined binding orientation in the binding groove of MD-2, which ensured tailored and species-independent (human and mice) TLR4 activation. Manipulating phosphorylation and acylation pattern at the sugar moiety facing the secondary dimerization interface allowed for adjustable modulation of the TLR4-mediated signaling. Tailored modulation of cellular pro-inflammatory responses by distinct modifications of the molecular structure of DLAMs was attained in primary human and mouse immune cells, lung epithelial cells and TLR4 transfected HEK293 cells.
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Affiliation(s)
- Holger Heine
- Research Group Innate Immunity, Research Center Borstel - Leibniz Lung Center, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Germany
| | - Florian Adanitsch
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Tina Tinkara Peternelj
- Department of Biotechnology, National Institute of Chemistry, University of Ljubljana, Ljubljana, Slovenia
| | - Mira Haegman
- Unit of Molecular Signal Transduction in Inflammation, Department of Biomedical Molecular Biology, Ghent University, Center for Inflammation Research, VIB, Ghent, Belgium
| | | | - Simon Ittig
- Biozentrum University of Basel, Basel, Switzerland
| | - Rudi Beyaert
- Unit of Molecular Signal Transduction in Inflammation, Department of Biomedical Molecular Biology, Ghent University, Center for Inflammation Research, VIB, Ghent, Belgium
| | - Roman Jerala
- Department of Biotechnology, National Institute of Chemistry, University of Ljubljana, Ljubljana, Slovenia
| | - Alla Zamyatina
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
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28
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Abstract
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Coiled-coil protein
origami (CCPO) polyhedra are designed self-assembling
nanostructures constructed from coiled coil (CC)-forming modules connected
into a single chain. For testing new CCPO building modules, simpler
polyhedra could be used that should maintain most features relevant
to larger scaffolds. We show the design and characterization of nanoscale
single-chain triangles, composed of six concatenated parallel CC dimer-forming
segments connected by flexible linker peptides. The polypeptides self-assembled
in bacteria in agreement with the design, and the shape of the polypeptides
was confirmed with small-angle X-ray scattering. Fusion with split-fluorescent
protein domains was used as a functional assay in bacteria, based
on the discrimination between the correctly folded and misfolded nanoscale
triangles comprising correct, mismatched, or truncated modules. This
strategy was used to evaluate the optimal size of linkers between
CC segments which comprised eight amino acid residues.
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Affiliation(s)
- Sabina Božič Abram
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Helena Gradišar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
- EN-FIST Centre of Excellence, 1000 Ljubljana, Slovenia
| | - Jana Aupič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Adam R. Round
- EMBL Grenoble outstation, 38042 Grenoble, France
- School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire, United Kingdom
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
- EN-FIST Centre of Excellence, 1000 Ljubljana, Slovenia
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29
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Lapenta F, Aupič J, Vezzoli M, Strmšek Ž, Da Vela S, Svergun DI, Carazo JM, Melero R, Jerala R. Self-assembly and regulation of protein cages from pre-organised coiled-coil modules. Nat Commun 2021; 12:939. [PMID: 33574245 PMCID: PMC7878516 DOI: 10.1038/s41467-021-21184-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 01/13/2021] [Indexed: 11/09/2022] Open
Abstract
Coiled-coil protein origami (CCPO) is a modular strategy for the de novo design of polypeptide nanostructures. CCPO folds are defined by the sequential order of concatenated orthogonal coiled-coil (CC) dimer-forming peptides, where a single-chain protein is programmed to fold into a polyhedral cage. Self-assembly of CC-based nanostructures from several chains, similarly as in DNA nanotechnology, could facilitate the design of more complex assemblies and the introduction of functionalities. Here, we show the design of a de novo triangular bipyramid fold comprising 18 CC-forming segments and define the strategy for the two-chain self-assembly of the bipyramidal cage from asymmetric and pseudo-symmetric pre-organised structural modules. In addition, by introducing a protease cleavage site and masking the interfacial CC-forming segments in the two-chain bipyramidal cage, we devise a proteolysis-mediated conformational switch. This strategy could be extended to other modular protein folds, facilitating the construction of dynamic multi-chain CC-based complexes. Coiled-coil protein origami is a strategy for the de novo design of polypeptide nanostructures based on coiled-coil dimer forming peptides, where a single chain protein folds into a polyhedral cage. Here, the authors design a single-chain triangular bipyramid and also demonstrate that the bipyramid can be self-assembled as a heterodimeric complex, comprising pre-defined subunits.
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Affiliation(s)
- Fabio Lapenta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Jana Aupič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Marco Vezzoli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Žiga Strmšek
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | | | | | | | - Roberto Melero
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia. .,EN-FIST Centre of Excellence, Ljubljana, Slovenia.
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30
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Aupič J, Strmšek Ž, Lapenta F, Pahovnik D, Pisanski T, Drobnak I, Ljubetič A, Jerala R. Designed folding pathway of modular coiled-coil-based proteins. Nat Commun 2021; 12:940. [PMID: 33574262 PMCID: PMC7878764 DOI: 10.1038/s41467-021-21185-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/13/2021] [Indexed: 12/02/2022] Open
Abstract
Natural proteins are characterised by a complex folding pathway defined uniquely for each fold. Designed coiled-coil protein origami (CCPO) cages are distinct from natural compact proteins, since their fold is prescribed by discrete long-range interactions between orthogonal pairwise-interacting coiled-coil (CC) modules within a single polypeptide chain. Here, we demonstrate that CCPO proteins fold in a stepwise sequential pathway. Molecular dynamics simulations and stopped-flow Förster resonance energy transfer (FRET) measurements reveal that CCPO folding is dominated by the effective intra-chain distance between CC modules in the primary sequence and subsequent folding intermediates, allowing identical CC modules to be employed for multiple cage edges and thus relaxing CCPO cage design requirements. The number of orthogonal modules required for constructing a CCPO tetrahedron can be reduced from six to as little as three different CC modules. The stepwise modular nature of the folding pathway offers insights into the folding of tandem repeat proteins and can be exploited for the design of modular protein structures based on a given set of orthogonal modules.
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Affiliation(s)
- Jana Aupič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Žiga Strmšek
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Interdisciplinary Doctoral Programme in Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Fabio Lapenta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - David Pahovnik
- Department of Polymer Chemistry and Technology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Tomaž Pisanski
- FAMNIT, University of Primorska, Koper, Slovenia
- Institute of Mathematics, Physics and Mechanics, Ljubljana, Slovenia
| | - Igor Drobnak
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Ajasja Ljubetič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.
- EN-FIST Centre of Excellence, Ljubljana, Slovenia.
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31
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Qu JH, Leirs K, Escudero R, Strmšek Ž, Jerala R, Spasic D, Lammertyn J. Novel Regeneration Approach for Creating Reusable FO-SPR Probes with NTA Surface Chemistry. Nanomaterials (Basel) 2021; 11:186. [PMID: 33451032 PMCID: PMC7828519 DOI: 10.3390/nano11010186] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 12/15/2022]
Abstract
To date, surface plasmon resonance (SPR) biosensors have been exploited in numerous different contexts while continuously pushing boundaries in terms of improved sensitivity, specificity, portability and reusability. The latter has attracted attention as a viable alternative to disposable biosensors, also offering prospects for rapid screening of biomolecules or biomolecular interactions. In this context here, we developed an approach to successfully regenerate a fiber-optic (FO)-SPR surface when utilizing cobalt (II)-nitrilotriacetic acid (NTA) surface chemistry. To achieve this, we tested multiple regeneration conditions that can disrupt the NTA chelate on a surface fully saturated with His6-tagged antibody fragments (scFv-33H1F7) over ten regeneration cycles. The best surface regeneration was obtained when combining 100 mM EDTA, 500 mM imidazole and 0.5% SDS at pH 8.0 for 1 min with shaking at 150 rpm followed by washing with 0.5 M NaOH for 3 min. The true versatility of the established approach was proven by regenerating the NTA surface for ten cycles with three other model system bioreceptors, different in their size and structure: His6-tagged SARS-CoV-2 spike fragment (receptor binding domain, RBD), a red fluorescent protein (RFP) and protein origami carrying 4 RFPs (Tet12SN-RRRR). Enabling the removal of His6-tagged bioreceptors from NTA surfaces in a fast and cost-effective manner can have broad applications, spanning from the development of biosensors and various biopharmaceutical analyses to the synthesis of novel biomaterials.
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Affiliation(s)
- Jia-Huan Qu
- Biosensors Group, Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium; (J.-H.Q.); (K.L.); (R.E.)
| | - Karen Leirs
- Biosensors Group, Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium; (J.-H.Q.); (K.L.); (R.E.)
| | - Remei Escudero
- Biosensors Group, Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium; (J.-H.Q.); (K.L.); (R.E.)
| | - Žiga Strmšek
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia; (Ž.S.); (R.J.)
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia; (Ž.S.); (R.J.)
| | - Dragana Spasic
- Biosensors Group, Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium; (J.-H.Q.); (K.L.); (R.E.)
| | - Jeroen Lammertyn
- Biosensors Group, Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium; (J.-H.Q.); (K.L.); (R.E.)
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Verbič A, Praznik A, Jerala R. A guide to the design of synthetic gene networks in mammalian cells. FEBS J 2020; 288:5265-5288. [PMID: 33289352 DOI: 10.1111/febs.15652] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/06/2020] [Accepted: 11/01/2020] [Indexed: 12/22/2022]
Abstract
Synthetic biology aims to harness natural and synthetic biological parts and engineering them in new combinations and systems, producing novel therapies, diagnostics, bioproduction systems, and providing information on the mechanism of function of biological systems. Engineering cell function requires the rewiring or de novo construction of cell information processing networks. Using natural and synthetic signal processing elements, researchers have demonstrated a wide array of signal sensing, processing and propagation modules, using transcription, translation, or post-translational modification to program new function. The toolbox for synthetic network design is ever-advancing and has still ample room to grow. Here, we review the diversity of synthetic gene networks, types of building modules, techniques of regulation, and their applications.
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Affiliation(s)
- Anže Verbič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Arne Praznik
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
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33
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Corcoran SE, Hafner-Bratkovič I, Halai R, Domingo-Fernandez R, O'Leary D, Banahan K, Jerala R, Conlon N, Jung T, O'Neill LA, Cooper MA, Irvine AD. The NLRP3 inhibitor MCC950 inhibits IL-1β production in PBMC from 19 patients with Cryopyrin-Associated Periodic Syndrome and in 2 patients with Schnitzler’s Syndrome. Wellcome Open Res 2020. [DOI: 10.12688/wellcomeopenres.16107.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background: The cryopyrin-associated periodic syndromes (CAPS) are a group of inherited disorders associated with systemic auto-inflammation. CAPS result from gain-of-function mutations in NLRP3, which result in formation of an intracellular protein complex known as the NLRP3 inflammasome. This leads to overproduction of IL-1β and other pro-inflammatory signals, resulting in inflammatory symptoms. Treatments for NLRP3-related diseases are biologic agents that directly target IL-1β. We sought to determine if the orally available small molecule NLRP3 inhibitor MCC950 could inhibit IL-1β ex vivo in a cohort of patients with autoinflammatory disease. Methods: Patients were recruited to donate blood, from which PBMCs were isolated and assayed in the presence of MCC950 to determine inhibitory efficacy. Results: We found that apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC) and mature IL-1β was higher in ex vivo PBMCs from CAPS patients than healthy donors. MCC950 inhibited production of mature IL-1β in PBMC from CAPS patients with a range of mutations and blocked NLRP3 activity in an in vitro mutation reconstitution assay. Similar results were observed with PBMC from two patients with Schnitzler’s Syndrome, another auto-inflammatory disease. Conclusions: The NLRP3 inflammasome inhibitor MCC950 blocked constitutive activation of NLRP3 observed in the PBMCs of CAPS patients. This study highlights the potential utility of NLRP3 inhibition by a small molecule for rare autoinflammatory diseases that are driven by NLRP3.
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Paveljšek D, Ivičak-Kocjan K, Treven P, Benčina M, Jerala R, Rogelj I. Distinctive probiotic features share common TLR2-dependent signalling in intestinal epithelial cells. Cell Microbiol 2020; 23:e13264. [PMID: 32945079 PMCID: PMC7757178 DOI: 10.1111/cmi.13264] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 09/11/2020] [Accepted: 09/13/2020] [Indexed: 12/14/2022]
Abstract
The underlying mechanisms of probiotics and postbiotics are not well understood, but it is known that both affect the adaptive and innate immune responses. In addition, there is a growing concept that some probiotic strains have common core mechanisms that provide certain health benefits. Here, we aimed to elucidate the signalization of the probiotic bacterial strains Lactobacillus paragasseri K7, Limosilactobacillus fermentum L930BB, Bifidobacterium animalis subsp. animalis IM386 and Lactiplantibacillus plantarum WCFS1. We showed in in vitro experiments that the tested probiotics exhibit common TLR2- and TLR10-dependent downstream signalling cascades involving inhibition of NF-κB signal transduction. Under inflammatory conditions, the probiotics activated phosphatidylinositol 3-kinase (PI3K)/Akt anti-apoptotic pathways and protein kinase C (PKC)-dependent pathways, which led to regulation of the actin cytoskeleton and tight junctions. These pathways contribute to the regeneration of the intestinal epithelium and modulation of the mucosal immune system, which, together with the inhibition of canonical TLR signalling, promote general immune tolerance. With this study we identified shared probiotic mechanisms and were the first to pinpoint the role of anti-inflammatory probiotic signalling through TLR10.
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Affiliation(s)
- Diana Paveljšek
- Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Domžale, Slovenia
| | - Karolina Ivičak-Kocjan
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Primož Treven
- Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Domžale, Slovenia
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Irena Rogelj
- Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Domžale, Slovenia
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Abstract
![]()
An important feature of synthetic
biological circuits is their
response to physicochemical signals, which enables the external control
of cellular processes. Calcium-dependent regulation is an attractive
approach for achieving such control, as diverse stimuli induce calcium
influx by activating membrane channel receptors. Most calcium-dependent
gene circuits use the endogenous nuclear factor of activated T-cells
(NFAT) signaling pathway. Here, we employed engineered NFAT transcription
factors to induce the potent and robust activation of exogenous gene
expression in HEK293T cells. Furthermore, we designed a calcium-dependent
transcription factor that does not interfere with NFAT-regulated promoters
and potently activates transcription in several mammalian cell types.
Additionally, we demonstrate that coupling the circuit to a calcium-selective
ion channel resulted in capsaicin- and temperature-controlled gene
expression. This engineered calcium-dependent signaling pathway enables
tightly controlled regulation of gene expression through different
stimuli in mammalian cells and is versatile, adaptable, and useful
for a wide range of therapeutic and diagnostic applications.
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Affiliation(s)
- Maja Meško
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
- Interfaculty Doctoral Study of Biomedicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Tina Lebar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Petra Dekleva
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Trg Osvobodilne fronte 13, SI-1000 Ljubljana, Slovenia
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Trg Osvobodilne fronte 13, SI-1000 Ljubljana, Slovenia
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36
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Lainšček D, Forstnerič V, Malenšek Š, Skrbinek M, Sever M, Jerala R. Abstract 4059: CRISPR-EXO - genetic deletion tool for treating chronic myelogenous leukemia. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-4059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Chronic myeloid leukemia (CML) is a myeloproliferative neoplastic disease, occurring in 1 to 2 cases per 100.000 adults, which accounts for ~ 15 % of newly diagnosed leukemias in adult patients. The diagnosis is based upon the genetic translocation between the t(9;22)(q34;q11.2), resulting in the formation of Philadelphia fusion chromosome, coding for BCR-ABL1 oncoprotein. The life-long treatment relies on tyrosine kinase inhibitors (TKIs). In nearly in 2 % patients develop point mutations, leading to resistance to TKIs treatment. New solutions for treating cancer with genetic etiology are considered. CRISPR/Cas system, composed of guide RNA, targeting endonuclease Cas9 to specific target genomic region has been used before to mediate breakage of Philadelphia chromosome at the site of oncogenic translocation. We present a strategy to couple Cas9 to the exonuclease to promote large deletions at the cancer-specific target genomic site. Cotransfection with EXOIII exhibited the best increase in deletion formation of all tested exonucleases. To further improve the rate of genetic lesion formation, Cas9 and EXOIII were connected via coiled-coil heterodimer forming peptides, bringing the two enzymes into close proximity (CRISPR-EXO). This resulted in a potent increase of deletion formation compared to the standard CRISPR/Cas, cotransfection and genetic fusion. We performed an animal study for the use of the CRISPR-EXO system as a potential anti-cancer therapeutic tool. In case of the CRISPR-EXO system, we showed a significant increase in cell death due to higher genome editing in the BCR-ABL1 region. These findings were confirmed also in an animal cancer model, where animals with tumors, electroporated with CRISPR-EXO system showed improved survival and drastic reduction in tumor size.CRISPR-EXO upgraded CRISPR system based on tethering Cas9 protein to exonuclease EXOIII by heterodimeric coiled-coil forming peptides, resulted in highly efficient editing of BCR-ABL1 fusion gene, leading to enhanced death of CML cancer cells.
Citation Format: Duško Lainšček, Vida Forstnerič, Špela Malenšek, Mojca Skrbinek, Matjaž Sever, Roman Jerala. CRISPR-EXO - genetic deletion tool for treating chronic myelogenous leukemia [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4059.
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Manček-Keber M, Ribić R, Chain F, Sinnaeve D, Martins JC, Jerala R, Tomić S, Fehér K. Adamantane Containing Peptidoglycan Fragments Enhance RANTES and IL-6 Production in Lipopolysaccharide-Induced Macrophages. Molecules 2020; 25:molecules25163707. [PMID: 32823878 PMCID: PMC7465286 DOI: 10.3390/molecules25163707] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 07/08/2020] [Accepted: 08/06/2020] [Indexed: 11/24/2022] Open
Abstract
We report the enhancement of the lipopolysaccharide-induced immune response by adamantane containing peptidoglycan fragments in vitro. The immune stimulation was detected by Il-6 (interleukine 6) and RANTES (regulated on activation, normal T cell expressed and secreted) chemokine expression using cell assays on immortalized mouse bone-marrow derived macrophages. The most active compound was a α-D-mannosyl derivative of an adamantylated tripeptide with L-chirality at the adamantyl group attachment, whereby the mannose moiety assumed to target mannose receptors expressed on macrophage cell surfaces. The immune co-stimulatory effect was also influenced by the configuration of the adamantyl center, revealing the importance of specific molecular recognition event taking place with its receptor. The immunostimulating activities of these compounds were further enhanced upon their incorporation into lipid bilayers, which is likely related to the presence of the adamantyl group that helps anchor the peptidoglycan fragment into lipid nanoparticles. We concluded that the proposed adamantane containing peptidoglycan fragments act as co-stimulatory agents and are also suitable for the preparation of lipid nanoparticle-based delivery of peptidoglycan fragments.
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Affiliation(s)
- Mateja Manček-Keber
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, P.O. Box 660, SI-1001 Ljubljana, Slovenia; (M.M.-K.); (R.J.)
- Centre of Excelence EN-FIST, SI-1000 Ljubljana, Slovenia
| | - Rosana Ribić
- University Center Varaždin, University North, Jurja Križanića 31b, HR-42 000 Varaždin, Croatia;
| | - Fernando Chain
- Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, 9000 Ghent, Belgium; (F.C.); (D.S.); (J.C.M.)
| | - Davy Sinnaeve
- Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, 9000 Ghent, Belgium; (F.C.); (D.S.); (J.C.M.)
- Univ. Lille, Inserm, Institut Pasteur de Lille, CHU Lille, U1167—Labex DISTALZ—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000 Lille, France
- CNRS, ERL9002—Integrative Structural Biology, F-59000 Lille, France
| | - José C. Martins
- Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, 9000 Ghent, Belgium; (F.C.); (D.S.); (J.C.M.)
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, P.O. Box 660, SI-1001 Ljubljana, Slovenia; (M.M.-K.); (R.J.)
- Centre of Excelence EN-FIST, SI-1000 Ljubljana, Slovenia
| | - Srđanka Tomić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102A, HR-10 000 Zagreb, Croatia;
| | - Krisztina Fehér
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
- Molecular Recognition and Interaction Research Group, Hungarian Academy of Sciences, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
- Correspondence: or ; Tel.: +36-52-512-900; Fax: +36-52-518-660
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Scalvini B, Sheikhhassani V, Woodard J, Aupič J, Dame RT, Jerala R, Mashaghi A. Topology of Folded Molecular Chains: From Single Biomolecules to Engineered Origami. Trends in Chemistry 2020. [DOI: 10.1016/j.trechm.2020.04.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Segal E, Zhang F, Lin X, King G, Shalem O, Shilo S, Allen WE, Alquaddoomi F, Altae-Tran H, Anders S, Balicer R, Bauman T, Bonilla X, Booman G, Chan AT, Cohen O, Coletti S, Davidson N, Dor Y, Drew DA, Elemento O, Evans G, Ewels P, Gale J, Gavrieli A, Geiger B, Grad YH, Greene CS, Hajirasouliha I, Jerala R, Kahles A, Kallioniemi O, Keshet A, Kocarev L, Landua G, Meir T, Muller A, Nguyen LH, Oresic M, Ovchinnikova S, Peterson H, Prodanova J, Rajagopal J, Rätsch G, Rossman H, Rung J, Sboner A, Sigaras A, Spector T, Steinherz R, Stevens I, Vilo J, Wilmes P. Publisher Correction: Building an international consortium for tracking coronavirus health status. Nat Med 2020; 26:1309. [PMID: 32591764 PMCID: PMC7319223 DOI: 10.1038/s41591-020-0983-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Eran Segal
- Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Feng Zhang
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xihong Lin
- Departments of Biostatistics and Statistics, Harvard T.H. Chan School of Public Health, Harvard University, Cambridge, MA, USA
| | - Gary King
- Institute for Quantitative Social Science, Harvard University, Cambridge, MA, USA
| | - Ophir Shalem
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Smadar Shilo
- Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.,Pediatric Diabetes Unit, Ruth Rappaport Children's Hospital, Rambam Healthcare Campus, Haifa, Israel
| | - William E Allen
- Harvard Society of Fellows, Harvard University, Cambridge, MA, USA
| | | | - Han Altae-Tran
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Simon Anders
- Center for Molecular Biology (ZMBH), University of Heidelberg, Heidelberg, Germany
| | - Ran Balicer
- Clalit Research Institute, Clalit Health Services, Ramat Gan, Israel
| | - Tal Bauman
- Mapping and Geo-Information Engineering, Civil and Environmental Engineering Faculty, The Technion, Haifa, Israel
| | - Ximena Bonilla
- ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | | | - Andrew T Chan
- Massachusetts General Hospital (MGH), Boston, MA, USA
| | - Ori Cohen
- Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Natalie Davidson
- ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Yuval Dor
- IMRIC Developmental Biology and Cancer Research, School of Medicine, The Hebrew University, Jerusalem, Israel
| | - David A Drew
- Massachusetts General Hospital (MGH), Boston, MA, USA
| | - Olivier Elemento
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.,Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Georgina Evans
- Institute for Quantitative Social Science, Harvard University, Cambridge, MA, USA
| | - Phil Ewels
- Science for Life Laboratory (SciLifeLab), Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | | | - Amir Gavrieli
- Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Benjamin Geiger
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Cambridge, MA, USA
| | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Iman Hajirasouliha
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.,Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Andre Kahles
- ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Olli Kallioniemi
- Science for Life Laboratory (SciLifeLab), Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Ayya Keshet
- Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ljupco Kocarev
- Macedonian Academy of Sciences and Arts, Skopje, Macedonia
| | | | - Tomer Meir
- Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Aline Muller
- Luxembourg Institute of Socio-Economic Research and University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Long H Nguyen
- Massachusetts General Hospital (MGH), Boston, MA, USA
| | - Matej Oresic
- School of Medical Sciences, Örebro University, Örebro, Sweden.,Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | | | - Hedi Peterson
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Jana Prodanova
- Macedonian Academy of Sciences and Arts, Skopje, Macedonia
| | - Jay Rajagopal
- Internal Medicine, Harvard Medical School, Boston, MA, USA.,Department of Pulmonary Medicine and Critical Care, Massachusetts General Hospital (MGH), Boston, MA, USA
| | - Gunnar Rätsch
- ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich and ELLIS Unit, ETH, Zurich, Switzerland
| | - Hagai Rossman
- Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Johan Rung
- Science for Life Laboratory (SciLifeLab), Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Andrea Sboner
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alexandros Sigaras
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.,Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | | | | | - Irene Stevens
- Science for Life Laboratory (SciLifeLab), Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jaak Vilo
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
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Lapenta F, Jerala R. Design of novel protein building modules and modular architectures. Curr Opin Struct Biol 2020; 63:90-96. [PMID: 32505942 DOI: 10.1016/j.sbi.2020.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 12/31/2022]
Abstract
Nature uses only a limited number of protein topologies and while several folds have evolved independently over time, there are clearly many possible topologies that have not been explored by evolution. With recent advances of protein design concepts, computational modeling tools, high resolution and high-throughput experimental methods it is now possible to design new protein architectures. The collection of building blocks and design principles widened both in size and complexity, offering an expanded toolset for building new modular folds and functional protein structures. Here we review and discuss recent achievements of protein design, focusing in particular on the use and prospects of modular approaches for assembling new protein folds.
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Affiliation(s)
- Fabio Lapenta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia; EN-FIST Centre of Excellence, Ljubljana, Slovenia.
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41
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Fink T, Stevović B, Verwaal R, Roubos JA, Gaber R, Benčina M, Jerala R, Gradišar H. Metabolic enzyme clustering by coiled coils improves the biosynthesis of resveratrol and mevalonate. AMB Express 2020; 10:97. [PMID: 32448937 PMCID: PMC7246283 DOI: 10.1186/s13568-020-01031-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 05/16/2020] [Indexed: 02/06/2023] Open
Abstract
The clustering of biosynthetic enzymes is used in nature to channel reaction products and increase the yield of compounds produced by multiple reaction steps. The coupling of multiple enzymes has been shown to increase the biosynthetic product yield. Different clustering strategies have particular advantages as the spatial organization of multiple enzymes creates biocatalytic cascades with a higher efficiency of biochemical reaction. However, there are also some drawbacks, such as misfolding and the variable stability of interaction domains, which may differ between particular biosynthetic reactions and the host organism. Here, we compared different protein-based clustering strategies, including direct fusion, fusion mediated by intein, and noncovalent interactions mediated through small coiled-coil dimer-forming domains. The clustering of enzymes through orthogonally designed coiled-coil interaction domains increased the production of resveratrol in Escherichia coli more than the intein-mediated fusion of biosynthetic enzymes. The improvement of resveratrol production correlated with the stability of the coiled-coil dimers. The coiled-coil fusion-based approach also increased mevalonate production in Saccharomyces cerevisiae, thus demonstrating the wider applicability of this strategy.
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Kadunc L, Svetličič M, Forstnerič V, Hafner Bratkovič I, Jerala R. Increased gene translation stringency in mammalian cells by nonsense suppression at multiple permissive sites with a single noncanonical amino acid. FEBS Lett 2020; 594:2452-2461. [PMID: 32401336 DOI: 10.1002/1873-3468.13810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/15/2020] [Accepted: 04/27/2020] [Indexed: 11/10/2022]
Abstract
The considerable potential of engineered cells compels the development of strategies for the stringent control of gene expression. A promising approach is the introduction of a premature stop codon (PTC) into a selected gene that is expressed only in the presence of noncanonical amino acids through nonsense suppression. Here, different strategies of amber PTC readthrough in mammalian cells were tested. The use of a tRNA synthetase together with a TAG codon-specific tRNA achieved PTC readthrough depending on the addition of a noncanonical amino acid (4-benzoyl-L-phenylalanine; Bpa). While single TAG codon incorporation exhibited detectable expression of the reporter protein even in the absence of Bpa, the use of a double PTC enabled virtually leakage-free functional gene translation. The introduction of an additional 5'-PTC, therefore, represents a generally applicable strategy to increase stringency in gene translation.
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Affiliation(s)
- Lucija Kadunc
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,Graduate School of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Svetličič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Vida Forstnerič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Iva Hafner Bratkovič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Ljubljana, Slovenia
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43
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Zhou W, Šmidlehner T, Jerala R. Synthetic biology principles for the design of protein with novel structures and functions. FEBS Lett 2020; 594:2199-2212. [PMID: 32324903 DOI: 10.1002/1873-3468.13796] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/29/2020] [Accepted: 04/03/2020] [Indexed: 12/14/2022]
Abstract
Nature provides a large number of functional proteins that evolved during billions of years of evolution. The diversity of natural proteins encompasses versatile functions and more than a thousand different folds, which, however, represents only a tiny fraction of all possible folds and polypeptide sequences. Recent advances in the rational design of proteins demonstrate that it is possible to design de novo protein folds unseen in nature. Novel protein topologies have been designed based on similar principles as natural proteins using advanced computational modelling or modular construction principles, such as oligomerization domains. Designed proteins exhibit several interesting features such as extreme stability, designability of 3D topologies and folding pathways. Moreover, designed protein assemblies can implement symmetry similar to the viral capsids, while, on the other hand, single-chain pseudosymmetric designs can address each position independently. Recently, the design is expanding towards the introduction of new functions into designed proteins, and we may soon be able to design molecular machines.
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Affiliation(s)
- Weijun Zhou
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Tamara Šmidlehner
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
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Ribić R, Manček-Keber M, Chain F, Sinnaeve D, Martins JC, Jerala R, Tomić S, Fehér K. Targeted Delivery of Adamantylated Peptidoglycan Immunomodulators in Lipid Nanocarriers: NMR Shows That Cargo Fragments Are Available on the Surface. J Phys Chem B 2020; 124:4132-4145. [PMID: 32283934 DOI: 10.1021/acs.jpcb.0c00029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We present an in-depth investigation of the membrane interactions of peptidoglycan (PGN)-based immune adjuvants designed for lipid-based delivery systems using NMR spectroscopy. The derivatives contain a cargo peptidoglycan (PGN) dipeptide fragment and an adamantyl group, which serves as an anchor to the lipid bilayer. Furthermore, derivatives with a mannose group that can actively target cell surface receptors on immune cells are also studied. We showed that the targeting mannose group and the cargo PGN fragment are both available on the lipid bilayer surface, thereby enabling interactions with cognate receptors. We found that the nonmannosylated compounds are incorporated stronger into the lipid assemblies than the mannosylated ones, but the latter compounds penetrate deeper in the bilayer. This might be explained by stronger electrostatic interactions available for zwitterionic nonmannosylated derivatives as opposed to the compounds in which the charged N-terminus is capped by mannose groups. The higher incorporation efficiency of the nonmannosylated compounds correlated with a larger relative enhancement in immune stimulation activities upon lipid incorporation compared to that of the derivatives with the mannose group. The chirality of the adamantyl group also influenced the incorporation efficiency, which in turn correlated with membrane-associated conformations that affect possible intermolecular interactions with lipid molecules. These findings will help in improving the development of PGN-based immune adjuvants suitable for delivery in lipid nanoparticles.
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Affiliation(s)
- Rosana Ribić
- University Center Varaždin, University North, Jurja Križanića 31b, HR-42 000 Varaždin, Croatia.,Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Mateja Manček-Keber
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, P.O. Box 660, SI-1001 Ljubljana, Slovenia.,Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Fernando Chain
- Department of Organic and Macromolecular Chemistry, Ghent University, Campus Sterre S4, Krijgslaan 281, 9000 Ghent, Belgium
| | - Davy Sinnaeve
- Department of Organic and Macromolecular Chemistry, Ghent University, Campus Sterre S4, Krijgslaan 281, 9000 Ghent, Belgium.,Univ. Lille, Inserm, Institut Pasteur de Lille, CHU Lille, U1167 - Labex DISTALZ - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000 Lille, France.,CNRS, ERL9002 - Integrative Structural Biology, F-59000 Lille, France
| | - José C Martins
- Department of Organic and Macromolecular Chemistry, Ghent University, Campus Sterre S4, Krijgslaan 281, 9000 Ghent, Belgium
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, P.O. Box 660, SI-1001 Ljubljana, Slovenia
| | - Srđanka Tomić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102A, HR-10 000 Zagreb, Croatia
| | - Krisztina Fehér
- Department of Organic and Macromolecular Chemistry, Ghent University, Campus Sterre S4, Krijgslaan 281, 9000 Ghent, Belgium.,Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Molecular Recognition and Interaction Research Group, Hungarian Academy of Sciences, Egyetem tér 1, H-4032 Debrecen, Hungary
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Evavold CL, Hafner-Bratkovic I, Jerala R, Kagan JC. A genome-wide CRISPR/Cas9 screen identifies novel regulators of GSDMD pore formation in engineered macrophages. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.149.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Cleavage of gasdermin D (GSDMD) by inflammatory caspases results in pore formation at the plasma membrane. GSDMD pores are recognized to mediate pyroptotic lysis of the cell or direct translocation of IL-1 family cytokines from the cytosol into the extracellular space depending on the quantity of pores or duration of plasma membrane occupancy. Hyperactive cells display evidence of fewer GSDMD pores compared to their pyroptotic counterparts, and recent work suggests that ESCRT-dependent membrane repair pathways oppose the cell fate towards pyroptosis through removal of GSDMD pores from the plasma membrane. To identify regulators of GSDMD pore formation at the plasma membrane, we utilized a genome-wide CRISPR/Cas9 screening platform in immortalized bone marrow derived macrophages (iBMDMs). This screen uncovered novel regulators of GSDMD pore formation in the plasma membrane.
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Affiliation(s)
- Charles Lee Evavold
- 1Harvard Medical School and Division of Gastroenterology, Boston Children’s Hospital, Boston, MA
- 2Program in Immunology, Harvard Medical School, Boston, MA
| | - Iva Hafner-Bratkovic
- 1Harvard Medical School and Division of Gastroenterology, Boston Children’s Hospital, Boston, MA
- 3Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia, Slovenia
| | - Roman Jerala
- 3Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia, Slovenia
| | - Jonathan C. Kagan
- 1Harvard Medical School and Division of Gastroenterology, Boston Children’s Hospital, Boston, MA
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Forstnerič V, Oven I, Ogorevc J, Lainšček D, Praznik A, Lebar T, Jerala R, Horvat S. CRISPRa-mediated FOXP3 gene upregulation in mammalian cells. Cell Biosci 2019; 9:93. [PMID: 31832140 PMCID: PMC6873431 DOI: 10.1186/s13578-019-0357-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/15/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Forkhead box P3+ (FOXP3 +) regulatory T cells (Tregs) are a subset of lymphocytes, critical for the maintenance of immune homeostasis. Loss-of-function mutations of the FOXP3 gene in animal models and humans results in loss of differentiation potential into Treg cells and are responsible for several immune-mediated inflammatory diseases. Strategies of increasing FOXP3 expression represent a potential approach to increase the pool of Tregs within the lymphocyte population and may be employed in therapies of diverse autoimmune conditions. In the present study, a dCas9 CRISPR-based method was systematically employed to achieve upregulation and sustained high expression of endogenous FOXP3 in HEK293 and human Jurkat T cell lines through targeting of the core promotor, three known regulatory regions of the FOXP3 gene (CNS1-3), and two additional regions selected through extensive bioinformatics analysis (Cage1 and Cage2). RESULTS Using an activator-domain fusion based dCas9 transcription activator, robust upregulation of FOXP3 was achieved, and an optimal combination of single guide RNAs was selected, which exerted an additive effect on FOXP3 gene upregulation. Simultaneous targeting of FOXP3 and EOS, a transcription factor known to act in concert with FOXP3 in initiating a Treg phenotype, resulted in upregulation of FOXP3 downstream genes CD25 and TNFR2. When compared to ectopic expression of FOXP3 via plasmid electroporation, upregulation of endogenous FOXP3 via the Cas9-based method resulted in prolonged expression of FOXP3 in Jurkat cells. CONCLUSIONS Transfection of both HEK293 and Jurkat cells with dCas9-activators showed that regulatory regions downstream and upstream of FOXP3 promoter can be very potent transcription inducers in comparison to targeting the core promoter. While introduction of genes by conventional methods of gene therapy may involve a risk of insertional mutagenesis due to viral integration into the genome, transient up- or down-regulation of transcription by a CRISPR-dCas9 approach may resolve this safety concern. dCas9-based systems provide great promise in DNA footprint-free phenotype perturbations (perturbation without the risk of DNA damage) to drive development of transcription modulation-based therapies.
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Affiliation(s)
- Vida Forstnerič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Irena Oven
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, 1230 Domžale, Slovenia
| | - Jernej Ogorevc
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, 1230 Domžale, Slovenia
| | - Duško Lainšček
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Arne Praznik
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Tina Lebar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Hajdrihova 19, 1000 Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Trg Osvobodilne fronte 13, 1000 Ljubljana, Slovenia
| | - Simon Horvat
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, 1230 Domžale, Slovenia
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47
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Majerle A, Schmieden DT, Jerala R, Meyer AS. Synthetic Biology for Multiscale Designed Biomimetic Assemblies: From Designed Self-Assembling Biopolymers to Bacterial Bioprinting. Biochemistry 2019; 58:2095-2104. [PMID: 30957491 DOI: 10.1021/acs.biochem.8b00922] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nature is based on complex self-assembling systems that span from the nanoscale to the macroscale. We have already begun to design biomimetic systems with properties that have not evolved in nature, based on designed molecular interactions and regulation of biological systems. Synthetic biology is based on the principle of modularity, repurposing diverse building modules to design new types of molecular and cellular assemblies. While we are currently able to use techniques from synthetic biology to design self-assembling molecules and re-engineer functional cells, we still need to use guided assembly to construct biological assemblies at the macroscale. We review the recent strategies for designing biological systems ranging from molecular assemblies based on self-assembly of (poly)peptides to the guided assembly of patterned bacteria, spanning 7 orders of magnitude.
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Affiliation(s)
- Andreja Majerle
- Department of Synthetic Biology and Immunology , National Institute of Chemistry , Hajdrihova 19 , 1000 Ljubljana , Slovenia
| | - Dominik T Schmieden
- Department of Bionanoscience, Kavli Institute of Nanoscience , Delft University of Technology , 2629 HZ Delft , The Netherlands
| | - Roman Jerala
- Department of Synthetic Biology and Immunology , National Institute of Chemistry , Hajdrihova 19 , 1000 Ljubljana , Slovenia
| | - Anne S Meyer
- Department of Biology , University of Rochester , Rochester , New York 14627 , United States
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48
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Golob-Urbanc A, Rajčević U, Strmšek Ž, Jerala R. Design of split superantigen fusion proteins for cancer immunotherapy. J Biol Chem 2019; 294:6294-6305. [PMID: 30782846 DOI: 10.1074/jbc.ra118.006742] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/26/2019] [Indexed: 11/06/2022] Open
Abstract
Several antibody-targeting cancer immunotherapies have been developed based on T cell activation at the target cells. One of the most potent activators of T cells are bacterial superantigens, which bind to major histocompatibility complex class II on antigen-presenting cells and activate T cells through T cell receptor. Strong T cell activation is also one of the main weaknesses of this strategy as it may lead to systemic T cell activation. To overcome the limitation of conventional antibody-superantigen fusion proteins, we have split a superantigen into two fragments, individually inactive, until both fragments came into close proximity and reassembled into a biologically active form capable of activating T cell response. A screening method based on fusion between SEA and coiled-coil heterodimers was developed that enabled detection of functional split SEA designs. The split SEA design that demonstrated efficacy in fusion with coiled-coil dimer forming polypeptides was fused to a single chain antibody specific for tumor antigen CD20. This design selectively activated T cells by split SEA-scFv fusion binding to target cells.
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Affiliation(s)
- Anja Golob-Urbanc
- From the Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.,Graduate School of Biomedicine, University of Ljubljana, 1000 Ljubljana, Slovenia, and
| | - Uroš Rajčević
- Department of Research and Development, Blood Transfusion Centre of Slovenia, Šlajmerjeva 6, 1000 Ljubljana, Slovenia
| | - Žiga Strmšek
- From the Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.,Graduate School of Biomedicine, University of Ljubljana, 1000 Ljubljana, Slovenia, and
| | - Roman Jerala
- From the Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia,
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49
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Fink T, Lonzarić J, Praznik A, Plaper T, Merljak E, Leben K, Jerala N, Lebar T, Strmšek Ž, Lapenta F, Benčina M, Jerala R. Design of fast proteolysis-based signaling and logic circuits in mammalian cells. Nat Chem Biol 2019; 15:115-122. [PMID: 30531965 PMCID: PMC7069760 DOI: 10.1038/s41589-018-0181-6] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/05/2018] [Indexed: 01/05/2023]
Abstract
Cellular signal transduction is predominantly based on protein interactions and their post-translational modifications, which enable a fast response to input signals. Owing to difficulties in designing new unique protein-protein interactions, designed cellular logic has focused on transcriptional regulation; however, that process has a substantially slower response, because it requires transcription and translation. Here, we present de novo design of modular, scalable signaling pathways based on proteolysis and designed coiled coils (CC) and implemented in mammalian cells. A set of split proteases with highly specific orthogonal cleavage motifs was constructed and combined with strategically positioned cleavage sites and designed orthogonal CC dimerizing domains with tunable affinity for competitive displacement after proteolytic cleavage. This framework enabled the implementation of Boolean logic functions and signaling cascades in mammalian cells. The designed split-protease-cleavable orthogonal-CC-based (SPOC) logic circuits enable response to chemical or biological signals within minutes rather than hours and should be useful for diverse medical and nonmedical applications.
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Affiliation(s)
- Tina Fink
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Jan Lonzarić
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Arne Praznik
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tjaša Plaper
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Estera Merljak
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Katja Leben
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Nina Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Tina Lebar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Žiga Strmšek
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Fabio Lapenta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- ENFIST Centre of Excellence, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.
- ENFIST Centre of Excellence, Ljubljana, Slovenia.
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50
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Cochet F, Facchini FA, Zaffaroni L, Billod JM, Coelho H, Holgado A, Braun H, Beyaert R, Jerala R, Jimenez-Barbero J, Martin-Santamaria S, Peri F. Novel carboxylate-based glycolipids: TLR4 antagonism, MD-2 binding and self-assembly properties. Sci Rep 2019; 9:919. [PMID: 30696900 PMCID: PMC6351529 DOI: 10.1038/s41598-018-37421-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 11/14/2018] [Indexed: 12/31/2022] Open
Abstract
New monosaccharide-based lipid A analogues were rationally designed through MD-2 docking studies. A panel of compounds with two carboxylate groups as phosphates bioisosteres, was synthesized with the same glucosamine-bis-succinyl core linked to different unsaturated and saturated fatty acid chains. The binding of the synthetic compounds to purified, functional recombinant human MD-2 was studied by four independent methods. All compounds bound to MD-2 with similar affinities and inhibited in a concentration-dependent manner the LPS-stimulated TLR4 signaling in human and murine cells, while being inactive as TLR4 agonists when provided alone. A compound of the panel was tested in vivo and was not able to inhibit the production of proinflammatory cytokines in animals. This lack of activity is probably due to strong binding to serum albumin, as suggested by cell experiments in the presence of the serum. The interesting self-assembly property in solution of this type of compounds was investigated by computational methods and microscopy, and formation of large vesicles was observed by cryo-TEM microscopy.
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Affiliation(s)
- Florent Cochet
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20126, Milano, Italy
| | - Fabio A Facchini
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20126, Milano, Italy
| | - Lenny Zaffaroni
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20126, Milano, Italy
| | - Jean-Marc Billod
- Department of Structural and Chemical Biology, Centro de Investigaciones Biologicas, CIB-CSIC, Ramiro de Maeztu, 9, 28040, Madrid, Spain
| | - Helena Coelho
- Molecular Recognition & Host-Pathogen Interactions Programme, CIC bioGUNE, Bizkaia Technology Park, Building 801 A, 48170, Derio, Spain.,UCIBIO, REQUIMTE, Departamento de Quimica, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.,Department of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, 48940, Leioa, Bizkaia, Spain
| | - Aurora Holgado
- Unit for Molecular Signal Transduction in Inflammation VIB-UGent Center for Inflammation Research, VIB Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium
| | - Harald Braun
- Unit for Molecular Signal Transduction in Inflammation VIB-UGent Center for Inflammation Research, VIB Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium
| | - Rudi Beyaert
- Unit for Molecular Signal Transduction in Inflammation VIB-UGent Center for Inflammation Research, VIB Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium
| | - Roman Jerala
- Department of Biotechnology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Jesus Jimenez-Barbero
- Molecular Recognition & Host-Pathogen Interactions Programme, CIC bioGUNE, Bizkaia Technology Park, Building 801 A, 48170, Derio, Spain.,Department of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, 48940, Leioa, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 13, 48009, Bilbao, Spain
| | - Sonsoles Martin-Santamaria
- Department of Structural and Chemical Biology, Centro de Investigaciones Biologicas, CIB-CSIC, Ramiro de Maeztu, 9, 28040, Madrid, Spain
| | - Francesco Peri
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20126, Milano, Italy.
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