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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: 19] [Impact Index Per Article: 3.8] [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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52
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Lebar T, Verbič A, Ljubetič A, Jerala R. Polarized displacement by transcription activator-like effectors for regulatory circuits. Nat Chem Biol 2019; 15:80-87. [PMID: 30455466 DOI: 10.1038/s41589-018-0163-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 10/05/2018] [Indexed: 01/26/2023]
Abstract
The interplay between DNA-binding proteins plays an important role in transcriptional regulation and could increase the precision and complexity of designed regulatory circuits. Here we show that a transcription activator-like effector (TALE) can displace another TALE protein from DNA in a highly polarized manner, displacing only the 3'- but not 5'-bound overlapping or adjacent TALE. We propose that the polarized displacement by TALEs is based on its multipartite nature of binding to DNA. The polarized TALE displacement provides strategies for the specific regulation of gene expression, for construction of all two-input Boolean genetic logic circuits based on the robust propagation of the displacement across multiple neighboring sites, for displacement of zinc finger-based transcription factors and for suppression of Cas9-gRNA-mediated genome cleavage, enriching the synthetic biology toolbox and contributing to the understanding of the underlying principles of the facilitated displacement.
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Affiliation(s)
- Tina Lebar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Anže Verbič
- 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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53
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Lainšček D, Kadunc L, Keber MM, Bratkovič IH, Romih R, Jerala R. Delivery of an Artificial Transcription Regulator dCas9-VPR by Extracellular Vesicles for Therapeutic Gene Activation. ACS Synth Biol 2018; 7:2715-2725. [PMID: 30513193 DOI: 10.1021/acssynbio.8b00192] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [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: 01/18/2023]
Abstract
The CRISPR/Cas system has been developed as a potent tool for genome engineering and transcription regulation. However, the efficiency of the delivery of the system into cells, particularly for therapeutic in vivo applications, remains a major bottleneck. Extracellular vesicles (EVs), released by eukaryotic cells, can mediate the transfer of various molecules, including nucleic acids and proteins. We show the packaging and delivery of the CRISPR/Cas system via EVs to the target cells, combining the advantages of both technological platforms. A genome editing with designed extracellular vesicles (GEDEX) system generated by the producer cells can transfer the designed transcriptional regulator dCas9-VPR complexed with appropriate targeting gRNAs enabling activation of gene transcription. We show functional delivery in mammalian cells as well in the animals. The therapeutic efficiency of in vivo delivery of dCas9-VPR/sgRNA GEDEX is demonstrated in a mouse model of liver damage counteracted by upregulation of the endogenous hepatocyte growth factor, demonstrating the potential for therapeutic applications.
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Affiliation(s)
- Duško Lainšček
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia
| | - Lucija Kadunc
- 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
| | - Mateja Manček Keber
- 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
| | - Iva Hafner Bratkovič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia
| | - Rok Romih
- Institute of Cell Biology, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 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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54
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Hafner-Bratkovič I, Sušjan P, Lainšček D, Tapia-Abellán A, Cerović K, Kadunc L, Angosto-Bazarra D, Pelegrin P, Jerala R. NLRP3 lacking the leucine-rich repeat domain can be fully activated via the canonical inflammasome pathway. Nat Commun 2018; 9:5182. [PMID: 30518920 PMCID: PMC6281599 DOI: 10.1038/s41467-018-07573-4] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [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: 01/30/2018] [Accepted: 11/08/2018] [Indexed: 11/23/2022] Open
Abstract
NLRP3 is a cytosolic sensor triggered by different pathogen- and self-derived signals that plays a central role in a variety of pathological conditions, including sterile inflammation. The leucine-rich repeat domain is present in several innate immune receptors, where it is frequently responsible for sensing danger signals and regulation of activation. Here we show by reconstitution of truncated and chimeric variants into Nlrp3−/− macrophages that the leucine-rich repeat domain is dispensable for activation and self-regulation of NLRP3 by several different triggers. The pyrin domain on the other hand is required to maintain NLRP3 in the inactive conformation. A fully responsive minimal NLRP3 truncation variant reconstitutes peritonitis in Nlrp3−/− mice. We demonstrate that in contrast to pathogen-activated NLRC4, the constitutively active NLRP3 molecule cannot engage wild-type NLRP3 molecules in a self-catalytic oligomerization. This lack of signal amplification is likely a protective mechanism to decrease sensitivity to endogenous triggers to impede autoinflammation. Activation of the NLRP3 inflammasome is associated with various diseases but its activation mechanism is not fully understood. Here, the authors determine the impact of different NLRP3 domains on sensing NLRP3 triggers, inflammasome assembly and regulation of NLRP3 inflammasome activation.
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Affiliation(s)
- Iva Hafner-Bratkovič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia. .,EN-FIST Centre of Excellence, Trg Osvobodilne fronte 13, 1000, Ljubljana, Slovenia.
| | - Petra Sušjan
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Duško Lainšček
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Ana Tapia-Abellán
- Molecular Inflammation Group, Biomedical Research Institute of Murcia (IMIB-Arrixaca), University Clinical Hospital Virgen de la Arrixaca, Carretera Buenavista s/n, 30120 El Palmar, Murcia, Spain
| | - Kosta Cerović
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Lucija Kadunc
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Diego Angosto-Bazarra
- Molecular Inflammation Group, Biomedical Research Institute of Murcia (IMIB-Arrixaca), University Clinical Hospital Virgen de la Arrixaca, Carretera Buenavista s/n, 30120 El Palmar, Murcia, Spain
| | - Pablo Pelegrin
- Molecular Inflammation Group, Biomedical Research Institute of Murcia (IMIB-Arrixaca), University Clinical Hospital Virgen de la Arrixaca, Carretera Buenavista s/n, 30120 El Palmar, Murcia, Spain
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia. .,EN-FIST Centre of Excellence, Trg Osvobodilne fronte 13, 1000, Ljubljana, Slovenia.
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55
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Pohar J, Lainšček D, Kunšek A, Cajnko MM, Jerala R, Benčina M. Publisher Correction: Phosphodiester backbone of the CpG motif within immunostimulatory oligodeoxynucleotides augments activation of Toll-like receptor 9. Sci Rep 2018; 8:355. [PMID: 29305575 PMCID: PMC5756238 DOI: 10.1038/s41598-017-17988-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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56
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Abstract
Conformational change of proteins in response to chemical or physical signals is the underlying principle of many regulatory and transport mechanisms in biological systems. The ability to design proteins the conformational state of which can be precisely and reversibly controlled would facilitate the development of molecular machines tailored for specific applications. Here we explore metal-binding site design to engineer a peptide-based conformational switch called SwitCCh that assembles into a homodimeric coiled-coil in response to the addition of ZnII ions or low pH. Addition of ZnII promoted formation of a parallel homodimer with an increase in thermal stability by more than 30 °C. The peptide could be reversibly cycled between the coiled-coil and random conformation. Furthermore, the SwitCCh peptide was orthogonal to the previously developed coiled-coil dimer set, indicating it could be used for regulated self-assembly of coiled-coil based nanostructures and materials.
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Affiliation(s)
- Jana Aupič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia.,Doctoral Study Programme in Chemical Sciences, University of Ljubljana, Večna pot 113, 1000, Ljubljana, Slovenia
| | - Fabio Lapenta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia.,Interdisciplinary Doctoral Programme in Biomedicine, University of Ljubljana, Kongresni trg 12, 1000, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Trg OF 13, 1000, Ljubljana, Slovenia
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57
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Abstract
Guest editors Rein Ulijn and Roman Jerala introduce the Peptide and protein nanotechnology themed issue of Chemical Society Reviews.
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Affiliation(s)
- Rein V Ulijn
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), New York, NY, USA
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58
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Ivičak-Kocjan K, Forstnerič V, Panter G, Jerala R, Benčina M. Extension and refinement of the recognition motif for Toll-like receptor 5 activation by flagellin. J Leukoc Biol 2018; 104:767-776. [PMID: 29920759 DOI: 10.1002/jlb.3vma0118-035r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 01/29/2018] [Revised: 04/24/2018] [Accepted: 05/16/2018] [Indexed: 11/07/2022] Open
Abstract
TLRs sense conserved and essential molecular components of microbes that invade multicellular organisms. The wide range of TLR agonists, differing in size and shape, is recognized either through a single or a pair of binding sites on the ectodomains of TLRs. TLR5 recognizes bacterial flagellin through two distinct binding sites on the ectodomain, the first facilitating primary binding of flagellin and the second guiding receptor dimerization necessary for signaling. The regions of flagellin recognized by TLR5 encompass key functional regions within the D1 domain of flagellin, which is also required for the assembly of functional flagella. In addition to previously identified binding sites at the N-terminal and central segment of the TLR5 ectodomain, we extended the TLR5'-D1 interaction interface on TLR5 and showed a species-specific recognition relevance of this extended region. In addition, we showed that the loop and following β-hairpin region of flagellin, previously proposed to participate in the TLR5-flagellin dimerization interface, is not accountable for these species-specific differences. We further identified residues that contribute to the interaction between two TLR5 ectodomains in an active signaling complex. Our work demonstrates that flagellin is recognized by TLR5 through a more extensive interaction surface than previously characterized.
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Affiliation(s)
- Karolina Ivičak-Kocjan
- 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
| | - Gabriela Panter
- 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
- Centre of Excellence EN-FIST, Ljubljana, Slovenia
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
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59
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Benčina M, Mori J, Gaber R, Jerala R. Metabolic Channeling Using DNA as a Scaffold. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch12] [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: 11/08/2022] Open
Affiliation(s)
- Mojca Benčina
- National Institute of Chemistry; Department of Biotechnology; Hajdrihova 19 SI1000 Ljubljana Slovenia
- Centre of Excellence EN-FIST; Trg Osvobodilne fronte 13 SI1000 Ljubljana Slovenia
| | - Jerneja Mori
- National Institute of Chemistry; Department of Biotechnology; Hajdrihova 19 SI1000 Ljubljana Slovenia
- Centre of Excellence EN-FIST; Trg Osvobodilne fronte 13 SI1000 Ljubljana Slovenia
| | - Rok Gaber
- National Institute of Chemistry; Department of Biotechnology; Hajdrihova 19 SI1000 Ljubljana Slovenia
- Centre of Excellence EN-FIST; Trg Osvobodilne fronte 13 SI1000 Ljubljana Slovenia
| | - Roman Jerala
- National Institute of Chemistry; Department of Biotechnology; Hajdrihova 19 SI1000 Ljubljana Slovenia
- Centre of Excellence EN-FIST; Trg Osvobodilne fronte 13 SI1000 Ljubljana Slovenia
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60
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Facchini FA, Zaffaroni L, Minotti A, Rapisarda S, Calabrese V, Forcella M, Fusi P, Airoldi C, Ciaramelli C, Billod JM, Schromm AB, Braun H, Palmer C, Beyaert R, Lapenta F, Jerala R, Pirianov G, Martin-Santamaria S, Peri F. Structure-Activity Relationship in Monosaccharide-Based Toll-Like Receptor 4 (TLR4) Antagonists. J Med Chem 2018; 61:2895-2909. [PMID: 29494148 DOI: 10.1021/acs.jmedchem.7b01803] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The structure-activity relationship was investigated in a series of synthetic TLR4 antagonists formed by a glucosamine core linked to two phosphate esters and two linear carbon chains. Molecular modeling showed that the compounds with 10, 12, and 14 carbons chains are associated with higher stabilization of the MD-2/TLR4 antagonist conformation than in the case of the C16 variant. Binding experiments with human MD-2 showed that the C12 and C14 variants have higher affinity than C10, while the C16 variant did not interact with the protein. The molecules, with the exception of the C16 variant, inhibited the LPS-stimulated TLR4 signal in human and murine cells, and the antagonist potency mirrored the MD-2 affinity calculated from in vitro binding experiments. Fourier-transform infrared, nuclear magnetic resonance, and small angle X-ray scattering measurements suggested that the aggregation state in aqueous solution depends on fatty acid chain lengths and that this property can influence TLR4 activity in this series of compounds.
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Affiliation(s)
- 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
| | - Alberto Minotti
- Department of Biotechnology and Biosciences , University of Milano-Bicocca , Piazza della Scienza, 2 , 20126 Milano , Italy
| | - Silvia Rapisarda
- Department of Biotechnology and Biosciences , University of Milano-Bicocca , Piazza della Scienza, 2 , 20126 Milano , Italy
| | - Valentina Calabrese
- Department of Biotechnology and Biosciences , University of Milano-Bicocca , Piazza della Scienza, 2 , 20126 Milano , Italy
| | - Matilde Forcella
- Department of Biotechnology and Biosciences , University of Milano-Bicocca , Piazza della Scienza, 2 , 20126 Milano , Italy
| | - Paola Fusi
- Department of Biotechnology and Biosciences , University of Milano-Bicocca , Piazza della Scienza, 2 , 20126 Milano , Italy
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences , University of Milano-Bicocca , Piazza della Scienza, 2 , 20126 Milano , Italy
| | - Carlotta Ciaramelli
- Department of Biotechnology and Biosciences , University of Milano-Bicocca , Piazza della Scienza, 2 , 20126 Milano , Italy
| | - Jean-Marc Billod
- Department of Structural & Chemical Biology , Centro de Investigaciones Biologicas, CIB-CSIC , C/Ramiro de Maeztu, 9 , 28040 Madrid , Spain
| | - Andra B Schromm
- Division of Immunobiophysics , Research Center Borstel , Parkallee 1-40 , 23845 Borstel , Germany
| | - Harald Braun
- VIB-UGent Center for Inflammation Research , UGent Department for Biomedical Molecular Biology, Unit of Molecular Signal Transduction in Inflammation , Technologiepark 927 , 9052 Ghent , Belgium
| | - Charys Palmer
- Anglia Ruskin Cambridge University , Cambridge CB1 1PT , U.K
| | - Rudi Beyaert
- VIB-UGent Center for Inflammation Research , UGent Department for Biomedical Molecular Biology, Unit of Molecular Signal Transduction in Inflammation , Technologiepark 927 , 9052 Ghent , Belgium
| | - Fabio Lapenta
- Department of Synthetic Biology and Immunology , Kemijski Institute, National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology , Kemijski Institute, National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia
| | - Grisha Pirianov
- Anglia Ruskin Cambridge University , Cambridge CB1 1PT , U.K
| | - Sonsoles Martin-Santamaria
- Department of Structural & Chemical Biology , Centro de Investigaciones Biologicas, CIB-CSIC , C/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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Murovec J, Guček K, Bohanec B, Avbelj M, Jerala R. DNA-Free Genome Editing of Brassica oleracea and B. rapa Protoplasts Using CRISPR-Cas9 Ribonucleoprotein Complexes. Front Plant Sci 2018; 9:1594. [PMID: 30455712 PMCID: PMC6230560 DOI: 10.3389/fpls.2018.01594] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 10/15/2018] [Indexed: 05/22/2023]
Abstract
The CRISPR/Cas9 genome editing system has already proved its efficiency, versatility and simplicity in numerous applications in human, animal, microbe and plant cells. Together with the vast amount of genome and transcriptome databases available, it represents an enormous potential for plant breeding and research. Although most changes produced with CRISPR/Cas9 do not differ from naturally occurring mutations, the use of transgenesis during varietal development can still trigger GMO legislation in countries that rely on process-based regulation. Moreover, stable integration of DNA coding for genome-editing tools into plant genomes can result in insertional mutagenesis, while its prolonged expression can cause mutations in off-target sites. These pitfalls can be avoided with the delivery of preassembled ribonucleoprotein complexes (RNPs) composed of purified recombinant enzyme Cas9 and in vitro-transcribed or synthesized sgRNA. We therefore aimed to develop a DNA-free protocol for site-directed mutagenesis of three species of the genus Brassica (B. oleracea, B. napus, and B. rapa) with the use of RNPs. We chose cabbage, rapeseed and Chinese cabbage as species representatives and introduced RNPs into their protoplasts with PEG 4000. Four sgRNAs targeting two endogenous genes (the FRI and PDS genes, two sgRNAs per gene) were introduced into all three species. No mutations were detected after transfection of rapeseed protoplasts, while we obtained mutation frequencies of 0.09 to 2.25% and 1.15 to 24.51% in cabbage and Chinese cabbage, respectively. In both species, a positive correlation was displayed between the amount (7.5, 15, 30, and 60 μg) of Cas9 enzyme and sgRNA introduced and mutation frequency. Nucleotide changes (insertions and deletions) were detected 24 h after transfection and did not differ 72 h after transfection. They were species-, gene- and locus-dependent. In summary, we demonstrated the suitability of RNP transfection into B. oleracea and B. rapa protoplasts for high-efficiency indel induction of two endogenous genes. Due to the relatively high mutation frequencies detected (up to 24.51%), this study paves the way for regeneration of precisely mutated Brassica plants without the use of transgenesis.
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Affiliation(s)
- Jana Murovec
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- *Correspondence: Jana Murovec,
| | - Katja Guček
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Borut Bohanec
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Monika Avbelj
- 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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62
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Lapenta F, Aupič J, Strmšek Ž, Jerala R. Coiled coil protein origami: from modular design principles towards biotechnological applications. Chem Soc Rev 2018; 47:3530-3542. [DOI: 10.1039/c7cs00822h] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
This review illustrates the current state in designing coiled-coil-based proteins with an emphasis on coiled coil protein origami structures and their potential.
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Affiliation(s)
- Fabio Lapenta
- Department of Synthetic Biology and Immunology
- National Institute of Chemistry
- Ljubljana
- Slovenia
| | - 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
| | - Roman Jerala
- Department of Synthetic Biology and Immunology
- National Institute of Chemistry
- Ljubljana
- Slovenia
- EN-FIST Centre of Excellence
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63
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Abstract
Transcriptional regulation lies at the center of many cellular processes and is the result of cellular response to different external and internal signals. Control of transcription of selected genes enables an unprecedented access to shape the cellular response. While orthogonal transcription factors from bacteria, yeast, plants, or other cells have been used to introduce new cellular logic into mammalian cells, the discovery of designable modular DNA binding domains, such as Transcription Activator-Like Effectors (TALEs) and the CRISPR system, enable targeting of almost any selected DNA sequence. Fusion or conditional association of DNA targeting domain with transcriptional effector domains enables controlled regulation of almost any endogenous or ectopic gene. Moreover, the designed regulators can be linked into genetic circuits to implement complex responses, such as different types of Boolean functions and switches. In this chapter, we describe the protocols for achieving efficient transcriptional regulation with TALE- and CRISPR-based designed transcription factors in mammalian cells.
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Affiliation(s)
- Tina Lebar
- Department of Synthetic Biology and Immunology, Kemijski inštitut/National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, Kemijski inštitut/National Institute of Chemistry, Ljubljana, Slovenia.
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Abstract
Proteins are highly perfected natural molecular machines, owing their properties to the complex tertiary structures with precise spatial positioning of different functional groups that have been honed through millennia of evolutionary selection. The prospects of designing new molecular machines and structural scaffolds beyond the limits of natural proteins make design of new protein folds a very attractive prospect. However, de novo design of new protein folds based on optimization of multiple cooperative interactions is very demanding. As a new alternative approach to design new protein folds unseen in nature, folds can be designed as a mathematical graph, by the self-assembly of interacting polypeptide modules within the single chain. Orthogonal coiled-coil dimers seem like an ideal building module due to their shape, adjustable length, and above all their designability. Similar to the approach of DNA nanotechnology, where complex tertiary structures are designed from complementary nucleotide segments, a polypeptide chain composed of a precisely specified sequence of coiled-coil forming segments can be designed to self-assemble into polyhedral scaffolds. This modular approach encompasses long-range interactions that define complex tertiary structures. We envision that by expansion of the toolkit of building blocks and design strategies of the folding pathways protein origami technology will be able to construct diverse molecular machines.
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Affiliation(s)
- Igor Drobnak
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Ajasja Ljubetič
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Helena Gradišar
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Tomaž Pisanski
- Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia.,University of Primorska, Koper, Slovenia
| | - Roman Jerala
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia. .,EN-FIST Centre of Excellence, Ljubljana, Slovenia.
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Ljubetič A, Lapenta F, Gradišar H, Drobnak I, Aupič J, Strmšek Ž, Lainšček D, Hafner-Bratkovič I, Majerle A, Krivec N, Benčina M, Pisanski T, Veličković TĆ, Round A, Carazo JM, Melero R, Jerala R. Design of coiled-coil protein-origami cages that self-assemble in vitro and in vivo. Nat Biotechnol 2017; 35:1094-1101. [DOI: 10.1038/nbt.3994] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 09/25/2017] [Indexed: 12/13/2022]
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Forstnerič V, Ivičak-Kocjan K, Plaper T, Jerala R, Benčina M. The role of the C-terminal D0 domain of flagellin in activation of Toll like receptor 5. PLoS Pathog 2017; 13:e1006574. [PMID: 28827825 PMCID: PMC5578693 DOI: 10.1371/journal.ppat.1006574] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 08/31/2017] [Accepted: 08/09/2017] [Indexed: 11/19/2022] Open
Abstract
Flagellin is a wide-spread bacterial virulence factor sensed by the membrane-bound Toll-like receptor 5 (TLR5) and by the intracellular NAIP5/NLRC4 inflammasome receptor. TLR5 recognizes a conserved region within the D1 domain of flagellin, crucial for the interaction between subunits in the flagellum and for bacterial motility. While it is known that a deletion of the D0 domain of flagellin, which lines the interior of flagella, also completely abrogates activation of TLR5, its functional role remains unknown. Using a protein fusion strategy, we propose a role for the D0 domain in the stabilization of an active dimeric signaling complex of flagellin-TLR5 at a 2:2 stoichiometric ratio. Alanine-scanning mutagenesis of flagellin revealed a previously unidentified region of flagellin, the C-terminal D0 domain, to play a crucial role in TLR5 activation. Interestingly, we show that TLR5 recognizes the same hydrophobic motif of the D0 domain of flagellin as the intracellular NAIP5/NLRC4 inflammasome receptor. Further, we show that residues within the D0 domain play a previously unrecognized role in the evasion of TLR5 recognition by Helicobacter pylori. These findings demonstrate that TLR5 is able to simultaneously sense several spatially separated sites of flagellin that are essential for its functionality, hindering bacterial evasion of immune recognition. Our findings significantly contribute to the understanding of the mechanism of TLR5 activation, which plays an important role in host defense against several pathogens, but also in several diseases, such as Crohn’s disease, cystic fibrosis and rheumatoid arthritis. Receptors of the innate immune system typically recognize conserved microbial patterns, crucial for pathogen fitness and survival. Flagellin, the main structural protein of bacterial flagella, is recognized by two receptors of the innate immune system, the intracellular inflammasome receptor NAIP5/NLRC4 and the membrane-bound Toll-like receptor 5. Ligand-induced dimerization is a crucial step in Toll-like receptor 5 activation. A crystal structure of segments of the ligand-bound receptor revealed binding interfaces on the ligand and receptor, but failed to fully clarify the activation mechanism, since the D0 domain of flagellin, which is crucial for receptor activation, is missing in the structure. We propose a role for the D0 domain in receptor dimerization and pinpoint specific amino-acid residues within the D0 domain, which contribute to Toll-like receptor 5 activation. We show that Toll-like receptor 5 recognizes the same protein motif detected by the intracellular NAIP5/NLRC4 receptor. Our work represents an important advance in the understanding of the mechanism of activation of Toll-like receptor 5.
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Affiliation(s)
- Vida Forstnerič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Karolina Ivičak-Kocjan
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Tjaša Plaper
- 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
- Centre of Excellence EN-FIST, Ljubljana, Slovenia
- * E-mail: (RJ); (MB)
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- * E-mail: (RJ); (MB)
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Drobnak I, Gradišar H, Ljubetič A, Merljak E, Jerala R. Modulation of Coiled-Coil Dimer Stability through Surface Residues while Preserving Pairing Specificity. J Am Chem Soc 2017; 139:8229-8236. [PMID: 28553984 DOI: 10.1021/jacs.7b01690] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The coiled-coil dimer is a widespread protein structural motif and, due to its designability, represents an attractive building block for assembling modular nanostructures. The specificity of coiled-coil dimer pairing is mainly based on hydrophobic and electrostatic interactions between residues at positions a, d, e, and g of the heptad repeat. Binding affinity, on the other hand, can also be affected by surface residues that face away from the dimerization interface. Here we show how design of the local helical propensity of interacting peptides can be used to tune the stabilities of coiled-coil dimers over a wide range. By designing intramolecular charge pairs, regions of high local helical propensity can be engineered to form trigger sequences, and dimer stability is adjusted without changing the peptide length or any of the directly interacting residues. This general principle is demonstrated by a change in thermal stability by more than 30 °C as a result of only two mutations outside the binding interface. The same approach was successfully used to modulate the stabilities in an orthogonal set of coiled-coils without affecting their binding preferences. The stability effects of local helical propensity and peptide charge are well described by a simple linear model, which should help improve current coiled-coil stability prediction algorithms. Our findings enable tuning the stabilities of coiled-coil-based building modules match a diverse range of applications in synthetic biology and nanomaterials.
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Affiliation(s)
- Igor Drobnak
- Department of Synthetic Biology and Immunology, National Institute of Chemistry , Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Helena Gradišar
- 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
| | - Ajasja Ljubetič
- 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
| | - 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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69
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Pirher N, Pohar J, Manček-Keber M, Benčina M, Jerala R. Activation of cell membrane-localized Toll-like receptor 3 by siRNA. Immunol Lett 2017; 189:55-63. [PMID: 28392198 DOI: 10.1016/j.imlet.2017.03.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 03/30/2017] [Indexed: 11/25/2022]
Abstract
Small interfering RNA molecules (siRNA) are short dsRNAs that are used for different therapeutic applications. On the other hand, dsRNAs can bind to and activate cell RNA sensors and consequently trigger inflammatory response. Here we show that siRNA activates primary human endothelial cells and human lymphatic endothelial cells and that this response is inhibited by antibodies against TLR3. In contrast, the activation of human lymphatic endothelial cells by poly(I:C) was inhibited by bafilomycin but not by anti-TLR3 antibodies. Bafilomycin also inhibited poly(I:C) but not siRNA cell stimulation in TLR3-transfected HEK293. The response to siRNA required the expression of UNC93B1, which directs TLR3 to the surface of HEK293 cells. We propose that the engaged signaling pathway of TLR3 depends on the receptor localization and on the length of the dsRNA, where the activation of cell membrane TLR3 by short dsRNA leads to a predominantly proinflammatory response, whereas TLR3 activation in endosomal compartments by long dsRNA is characterized by the production of type I IFN. A molecular model suggests that the siRNA can bind to the binding sites of the TLR3 ectodomain and trigger receptor dimerization. These results contribute to understanding of the mechanism of side effects seen in the therapeutic application of naked, unmodified siRNA as a result of the activation of TLR3 localized at the plasma membrane.
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Affiliation(s)
- Nina Pirher
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Jelka Pohar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Mateja Manček-Keber
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia; Excellent NMR Future Innovation for Sustainable Technologies Centre of Excellence, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia; Excellent NMR Future Innovation for Sustainable Technologies Centre of Excellence, Ljubljana, Slovenia.
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70
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Pohar J, Yamamoto C, Fukui R, Cajnko MM, Miyake K, Jerala R, Benčina M. Selectivity of Human TLR9 for Double CpG Motifs and Implications for the Recognition of Genomic DNA. J Immunol 2017; 198:2093-2104. [PMID: 28115525 DOI: 10.4049/jimmunol.1600757] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 12/19/2016] [Indexed: 12/18/2022]
Abstract
TLR9 acts as a first-line host defense against pathogens recognizing DNA comprising unmethylated CpG motifs present in bacteria and viruses. Species- and sequence-specific recognition differences were demonstrated for TLR9 receptors. Activation of human (h)TLR9 requires a pair of closely positioned CpG motifs within oligodeoxyribonucleotides (ODNs), whereas mouse TLR9 is effectively activated by an ODN with a single CpG motif. Molecular model-directed mutagenesis identified two regions, site A and site B, as important for receptor activation. Amino acid residues Gln346 and Arg348 within site A contribute to the sequence-specific recognition by hTLR9 in determining the bias for two appropriately spaced CpG motifs within immunostimulatory ODNs. Mutation of Gln562 at site B, in combination with Gln346 and Arg348 mutations of mouse counterparts, increased activation of hTLR9 by mouse-specific ODN, mammalian genomic DNA, and bacterial DNA. We propose that the double CpG motif sequence-specificity of hTLR9 results in decreased activation by ODNs with a lower frequency of CpG motifs, such as from mammalian genomic DNA, which increases hTLR9 selectivity for pathogen versus host DNA.
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Affiliation(s)
- Jelka Pohar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
| | - Chikako Yamamoto
- Division of Innate Immunity, Department of Microbiology and Immunology, University of Tokyo, Minatoku, Tokyo 108-8639, Japan
| | - Ryutaro Fukui
- Division of Innate Immunity, Department of Microbiology and Immunology, University of Tokyo, Minatoku, Tokyo 108-8639, Japan
| | - Miša-Mojca Cajnko
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
| | - Kensuke Miyake
- Division of Innate Immunity, Department of Microbiology and Immunology, University of Tokyo, Minatoku, Tokyo 108-8639, Japan.,Laboratory of Innate Immunity, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Minatoku, Tokyo 108-8639, Japan; and
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia; .,EN-FIST Centre of Excellence, SI-1000 Ljubljana, Slovenia
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia; .,EN-FIST Centre of Excellence, SI-1000 Ljubljana, Slovenia
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71
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Smole A, Lainšček D, Bezeljak U, Horvat S, Jerala R. A Synthetic Mammalian Therapeutic Gene Circuit for Sensing and Suppressing Inflammation. Mol Ther 2017; 25:102-119. [PMID: 28129106 DOI: 10.1016/j.ymthe.2016.10.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [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: 05/27/2016] [Revised: 10/20/2016] [Accepted: 10/21/2016] [Indexed: 12/20/2022] Open
Abstract
Inflammation, which is a highly regulated host response against danger signals, may be harmful if it is excessive and deregulated. Ideally, anti-inflammatory therapy should autonomously commence as soon as possible after the onset of inflammation, should be controllable by a physician, and should not systemically block beneficial immune response in the long term. We describe a genetically encoded anti-inflammatory mammalian cell device based on a modular engineered genetic circuit comprising a sensor, an amplifier, a "thresholder" to restrict activation of a positive-feedback loop, a combination of advanced clinically used biopharmaceutical proteins, and orthogonal regulatory elements that linked modules into the functional device. This genetic circuit was autonomously activated by inflammatory signals, including endogenous cecal ligation and puncture (CLP)-induced inflammation in mice and serum from a systemic juvenile idiopathic arthritis (sIJA) patient, and could be reset externally by a chemical signal. The microencapsulated anti-inflammatory device significantly reduced the pathology in dextran sodium sulfate (DSS)-induced acute murine colitis, demonstrating a synthetic immunological approach for autonomous anti-inflammatory therapy.
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Affiliation(s)
- Anže Smole
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Duško Lainšček
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Urban Bezeljak
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Simon Horvat
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia; EN-FIST Centre of Excellence, 1000 Ljubljana, Slovenia; Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia; EN-FIST Centre of Excellence, 1000 Ljubljana, Slovenia.
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72
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Lebar T, Jerala R. Benchmarking of TALE- and CRISPR/dCas9-Based Transcriptional Regulators in Mammalian Cells for the Construction of Synthetic Genetic Circuits. ACS Synth Biol 2016; 5:1050-1058. [PMID: 27344932 DOI: 10.1021/acssynbio.5b00259] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [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: 11/30/2022]
Abstract
Transcriptional activator-like effector (TALE)- and CRISPR/Cas9-based designable recognition domains represent a technological breakthrough not only for genome editing but also for building designed genetic circuits. Both platforms are able to target rarely occurring DNA segments, even within complex genomes. TALE and dCas9 domains, genetically fused to transcriptional regulatory domains, can be used for the construction of engineered logic circuits. Here we benchmarked the performance of the two platforms, targeting the same DNA sequences, to compare their advantages for the construction of designed circuits in mammalian cells. Optimal targeting strands for repression and activation of dCas9-based designed transcription factors were identified; both platforms exhibited good orthogonality and were used to construct functionally complete NOR gates. Although the CRISPR/dCas9 system is clearly easier to construct, TALE-based activators were significantly stronger, and the TALE-based platform performed better, especially for the construction of layered circuits.
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Affiliation(s)
- Tina Lebar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry , 1000 Ljubljana, Slovenia
- EN-FIST Centre of Excellence , 1000 Ljubljana, Slovenia
- Graduate School of Biomedicine, 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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73
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Forstnerič V, Ivičak-Kocjan K, Ljubetič A, Jerala R, Benčina M. Distinctive Recognition of Flagellin by Human and Mouse Toll-Like Receptor 5. PLoS One 2016; 11:e0158894. [PMID: 27391968 PMCID: PMC4938411 DOI: 10.1371/journal.pone.0158894] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 06/22/2016] [Indexed: 11/23/2022] Open
Abstract
Toll-like receptor 5 (TLR5) is a receptor of the innate immune system that recognizes flagellin from certain bacterial species and triggers an inflammatory response. The Salmonella dublin flagellin in complex with zebrafish TLR5 has been crystallized previously. In the present study, we extrapolate the structure of this complex using structure-guided mutagenesis to determine the recognition modes of human and mouse TLR5 receptors and demonstrate species-specific differences in flagellin recognition. In general, the recognition mode of the mouse receptor can be said to be more robust in comparison to that of the human receptor. All-atom molecular dynamics simulation showed differences between the two receptors within the primary binding region. Using a functional motility assay, we show that although the highly conserved area of the flagellin analyzed in this study encompasses key structural requirements for flagella formation, a direct correlation between immune recognition and structure on the level of amino acid residues is not observed.
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Affiliation(s)
- Vida Forstnerič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Karolina Ivičak-Kocjan
- 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
- Centre of Excellence EN-FIST, Ljubljana, Slovenia
- * E-mail: (RJ); (MB)
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Centre of Excellence EN-FIST, Ljubljana, Slovenia
- * E-mail: (RJ); (MB)
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74
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Božič Abram S, Aupič J, Dražić G, Gradišar H, Jerala R. Coiled-coil forming peptides for the induction of silver nanoparticles. Biochem Biophys Res Commun 2016; 472:566-71. [DOI: 10.1016/j.bbrc.2016.03.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 03/09/2016] [Indexed: 12/27/2022]
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75
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Ljubetič A, Drobnak I, Gradišar H, Jerala R. Designing the structure and folding pathway of modular topological bionanostructures. Chem Commun (Camb) 2016; 52:5220-9. [PMID: 27001947 DOI: 10.1039/c6cc00421k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Polypeptides and polynucleotides are programmable natural polymers whose linear sequence can be easily designed and synthesized by the cellular transcription/translation machinery. Nature primarily uses proteins as the molecular machines and nucleic acids as the medium for the manipulation of heritable information. A protein's tertiary structure and function is defined by multiple cooperative weak long-range interactions that have been optimized through evolution. DNA nanotechnology uses orthogonal pairwise interacting modules of complementary nucleic acids as a strategy to construct defined complex 3D structures. A similar approach has recently been applied to protein design, using orthogonal dimerizing coiled-coil segments as interacting modules. When concatenated into a single polypeptide chain, they self-assemble into the 3D structure defined by the topology of interacting modules within the chain. This approach allows the construction of geometric polypeptide scaffolds, bypassing the folding problem of compact proteins by relying on decoupled pairwise interactions. However, the folding pathway still needs to be optimized in order to allow rapid self-assembly under physiological conditions. Again the modularity of designed topological structures can be used to define the rules that guide the folding pathway of long polymers, such as DNA, based on the stability and topology of connected building modules. This approach opens the way towards incorporation of designed foldamers in biological systems and their functionalization.
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Affiliation(s)
- A Ljubetič
- National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia.
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Ciaramelli C, Calabrese V, Sestito SE, Pérez-Regidor L, Klett J, Oblak A, Jerala R, Piazza M, Martín-Santamaría S, Peri F. Glycolipid-based TLR4 Modulators and Fluorescent Probes: Rational Design, Synthesis, and Biological Properties. Chem Biol Drug Des 2016; 88:217-29. [PMID: 26896420 DOI: 10.1111/cbdd.12749] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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: 10/03/2015] [Revised: 12/08/2015] [Accepted: 02/08/2016] [Indexed: 12/13/2022]
Abstract
The cationic glycolipid IAXO-102, a potent TLR4 antagonist targeting both MD-2 and CD14 co-receptors, has been used as scaffold to design new potential TLR4 modulators and fluorescent labels for the TLR4 receptor complex (membrane TLR4.MD-2 dimer and CD14). The primary amino group of IAXO-102, not involved in direct interaction with MD-2 and CD14 receptors, has been exploited to covalently attach a fluorescein (molecules 1 and 2) or to link two molecules of IAXO-102 through diamine and diammonium spacers, obtaining 'dimeric' molecules 3 and 4. The structure-based rational design of compounds 1-4 was guided by the optimization of MD-2 and CD14 binding. Compounds 1 and 2 inhibited TLR4 activation, in a concentration-dependent manner, and signaling in HEK-Blue TLR4 cells. The fluorescent labeling of murine macrophages by molecule 1 was inhibited by LPS and was also abrogated when cell surface proteins were digested by trypsin, thus suggesting an interaction of fluorescent probe 1 with membrane proteins of the TLR4 receptor system.
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Affiliation(s)
- Carlotta Ciaramelli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20126, Milano, Italy
| | - Valentina Calabrese
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20126, Milano, Italy
| | - Stefania E Sestito
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20126, Milano, Italy
| | - Lucia Pérez-Regidor
- Department of Chemistry and Biochemistry, Universidad CEU San Pablo, 28668-Boadilla del Monte, Madrid, Spain.,Department of Chemical and Physical Biology, Center for Biological Research, CIB-CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Javier Klett
- Department of Chemistry and Biochemistry, Universidad CEU San Pablo, 28668-Boadilla del Monte, Madrid, Spain.,Department of Chemical and Physical Biology, Center for Biological Research, CIB-CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Alja Oblak
- Department of Biotechnology, National Institute of Chemistry Ljubljana and EN-FIST Center of Excellence, Hajdrihova 19, SI-1001, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Biotechnology, National Institute of Chemistry Ljubljana and EN-FIST Center of Excellence, Hajdrihova 19, SI-1001, Ljubljana, Slovenia
| | - Matteo Piazza
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20126, Milano, Italy
| | - Sonsoles Martín-Santamaría
- Department of Chemistry and Biochemistry, Universidad CEU San Pablo, 28668-Boadilla del Monte, Madrid, Spain.,Department of Chemical and Physical Biology, Center for Biological Research, 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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Vašl J, Oblak A, Peternelj TT, Klett J, Martín-Santamaría S, Gioannini TL, Weiss JP, Jerala R. Molecular Basis of the Functional Differences between Soluble Human Versus Murine MD-2: Role of Val135 in Transfer of Lipopolysaccharide from CD14 to MD-2. J Immunol 2016; 196:2309-18. [PMID: 26826249 DOI: 10.4049/jimmunol.1502074] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 12/26/2015] [Indexed: 11/19/2022]
Abstract
Myeloid differentiation factor 2 (MD-2) is an extracellular protein, associated with the ectodomain of TLR4, that plays a critical role in the recognition of bacterial LPS. Despite high overall structural and functional similarity, human (h) and murine (m) MD-2 exhibit several species-related differences. hMD-2 is capable of binding LPS in the absence of TLR4, whereas mMD-2 supports LPS responsiveness only when mMD-2 and mTLR4 are coexpressed in the same cell. Previously, charged residues at the edge of the LPS binding pocket have been attributed to this difference. In this study, site-directed mutagenesis was used to explore the hydrophobic residues within the MD-2 binding pocket as the source of functional differences between hMD-2 and mMD-2. Whereas decreased hydrophobicity of residues 61 and 63 in the hMD-2 binding pocket retained the characteristics of wild-type hMD-2, a relatively minor change of valine to alanine at position 135 completely abolished the binding of LPS to the hMD-2 mutant. The mutant, however, retained the LPS binding in complex with TLR4 and also cell activation, resulting in a murine-like phenotype. These results were supported by the molecular dynamics simulation. We propose that the residue at position 135 of MD-2 governs the dynamics of the binding pocket and its ability to accommodate lipid A, which is allosterically affected by bound TLR4.
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Affiliation(s)
- Jožica Vašl
- Department of Biotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Alja Oblak
- Department of Biotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Tina T Peternelj
- Department of Biotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Javier Klett
- Center for Biological Research, Superior Council for Scientific Research, 28040 Madrid, Spain
| | | | - Theresa L Gioannini
- Inflammation Program, Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, IA 52241; Veterans Affairs Medical Center, Iowa City, IA 52246; and
| | - Jerrold P Weiss
- Inflammation Program, Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, IA 52241
| | - Roman Jerala
- Department of Biotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia; Excellent Nuclear Magnetic Resonance-Future Innovation for Sustainable Technologies Center of Excellence, 1000 Ljubljana, Slovenia
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78
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Lonzarić J, Lebar T, Majerle A, Manček-Keber M, Jerala R. Locked and proteolysis-based transcription activator-like effector (TALE) regulation. Nucleic Acids Res 2016; 44:1471-81. [PMID: 26748097 PMCID: PMC4756844 DOI: 10.1093/nar/gkv1541] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [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: 06/03/2015] [Accepted: 12/26/2015] [Indexed: 11/13/2022] Open
Abstract
Development of orthogonal, designable and adjustable transcriptional regulators is an important goal of synthetic biology. Their activity has been typically modulated through stimulus-induced oligomerization or interaction between the DNA-binding and activation/repression domain. We exploited a feature of the designable Transcription activator-like effector (TALE) DNA-binding domain that it winds around the DNA which allows to topologically prevent it from binding by intramolecular cyclization. This new approach was investigated through noncovalent ligand-induced cyclization or through a covalent split intein cyclization strategy, where the topological inhibition of DNA binding by cyclization and its restoration by a proteolytic release of the topologic constraint was expected. We show that locked TALEs indeed have diminished DNA binding and regain full transcriptional activity by stimulation with the rapamycin ligand or site-specific proteolysis of the peptide linker, with much higher level of activation than rapamycin-induced heterodimerization. Additionally, we demonstrated reversibility, activation of genomic targets and implemented logic gates based on combinations of protein cyclization, proteolytic cleavage and ligand-induced dimerization, where the strongest fold induction was achieved by the proteolytic cleavage of a repression domain from a linear TALE.
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Affiliation(s)
- Jan Lonzarić
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana 1000, Slovenia EN-FIST Centre of Excellence, Ljubljana 1000, Slovenia Graduate School of Biomedicine, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Tina Lebar
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana 1000, Slovenia EN-FIST Centre of Excellence, Ljubljana 1000, Slovenia Graduate School of Biomedicine, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Andreja Majerle
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana 1000, Slovenia
| | - Mateja Manček-Keber
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana 1000, Slovenia EN-FIST Centre of Excellence, Ljubljana 1000, Slovenia
| | - Roman Jerala
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana 1000, Slovenia EN-FIST Centre of Excellence, Ljubljana 1000, Slovenia
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79
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Pohar J, Lainšček D, Fukui R, Yamamoto C, Miyake K, Jerala R, Benčina M. Species-Specific Minimal Sequence Motif for Oligodeoxyribonucleotides Activating Mouse TLR9. J Immunol 2015; 195:4396-405. [PMID: 26416273 DOI: 10.4049/jimmunol.1500600] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 08/26/2015] [Indexed: 12/25/2022]
Abstract
Synthetic oligodeoxyribonucleotides (ODNs) containing unmethylated CpG recapitulate the activation of TLR9 by microbial DNA. ODNs are potent stimulators of the immune response in cells expressing TLR9. Despite extensive use of mice as experimental animals in basic and applied immunological research, the key sequence determinants that govern the activation of mouse TLR9 by ODNs have not been well defined. We performed a systematic investigation of the sequence motif of B class phosphodiester ODNs to identify the sequence properties that govern mouse TLR9 activation. In contrast to ODNs activating human TLR9, where the minimal sequence motif for the receptor activation comprises a pair of closely positioned CpGs we found that the mouse TLR9 requires a single CpG positioned 4-6 nt from the 5'-end. Activation is augmented by a 5'TCC sequence one to three nucleotides from the CG. The distance of the CG dinucleotide of four to six nucleotides from the 5'-end and the ODN's length fine-tunes activation of mouse macrophages. Length of the ODN <23 and >29 nt decreases activation of dendritic cells. The ODNs with minimal sequence induce Th1-type cytokine synthesis in dendritic cells and confirm the expression of cell surface markers in B cells. Identification of the minimal sequence provides an insight into the sequence selectivity of mouse TLR9 and points to the differences in the receptor selectivity between species probably as a result of differences in the receptor binding sites.
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Affiliation(s)
- Jelka Pohar
- Laboratory of Biotechnology, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
| | - Duško Lainšček
- Laboratory of Biotechnology, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
| | - Ryutaro Fukui
- Division of Innate Immunity, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Chikako Yamamoto
- Division of Innate Immunity, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Kensuke Miyake
- Division of Innate Immunity, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; Laboratory of Innate Immunity, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; and
| | - Roman Jerala
- Laboratory of Biotechnology, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia; EN-FIST Centre of Excellence, SI-1000 Ljubljana, Slovenia
| | - Mojca Benčina
- Laboratory of Biotechnology, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia; EN-FIST Centre of Excellence, SI-1000 Ljubljana, Slovenia
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80
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Di Lorenzo F, Kubik Ł, Oblak A, Lorè NI, Cigana C, Lanzetta R, Parrilli M, Hamad MA, De Soyza A, Silipo A, Jerala R, Bragonzi A, Valvano MA, Martín-Santamaría S, Molinaro A. Activation of Human Toll-like Receptor 4 (TLR4)·Myeloid Differentiation Factor 2 (MD-2) by Hypoacylated Lipopolysaccharide from a Clinical Isolate of Burkholderia cenocepacia. J Biol Chem 2015; 290:21305-19. [PMID: 26160169 DOI: 10.1074/jbc.m115.649087] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Indexed: 11/06/2022] Open
Abstract
Lung infection by Burkholderia species, in particular Burkholderia cenocepacia, accelerates tissue damage and increases post-lung transplant mortality in cystic fibrosis patients. Host-microbe interplay largely depends on interactions between pathogen-specific molecules and innate immune receptors such as Toll-like receptor 4 (TLR4), which recognizes the lipid A moiety of the bacterial lipopolysaccharide (LPS). The human TLR4·myeloid differentiation factor 2 (MD-2) LPS receptor complex is strongly activated by hexa-acylated lipid A and poorly activated by underacylated lipid A. Here, we report that B. cenocepacia LPS strongly activates human TLR4·MD-2 despite its lipid A having only five acyl chains. Furthermore, we show that aminoarabinose residues in lipid A contribute to TLR4-lipid A interactions, and experiments in a mouse model of LPS-induced endotoxic shock confirmed the proinflammatory potential of B. cenocepacia penta-acylated lipid A. Molecular modeling combined with mutagenesis of TLR4-MD-2 interactive surfaces suggests that longer acyl chains and the aminoarabinose residues in the B. cenocepacia lipid A allow exposure of the fifth acyl chain on the surface of MD-2 enabling interactions with TLR4 and its dimerization. Our results provide a molecular model for activation of the human TLR4·MD-2 complex by penta-acylated lipid A explaining the ability of hypoacylated B. cenocepacia LPS to promote proinflammatory responses associated with the severe pathogenicity of this opportunistic bacterium.
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Affiliation(s)
- Flaviana Di Lorenzo
- From the Departments of Chemical Sciences and Department of Biotechnology, National Institute of Chemistry, Ljubljana 1000, Slovenia
| | - Łukasz Kubik
- Department of Chemistry and Biochemistry, Universidad CEU San Pablo, Boadilla del Monte, Madrid 28668, Spain, Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Gdańsk 80-416, Poland
| | - Alja Oblak
- Department of Biotechnology, National Institute of Chemistry, Ljubljana 1000, Slovenia, Centre of Excellence NMR - Future Innovation for Sustainable Technologies, Ljubljana 1000, Slovenia
| | - Nicola Ivan Lorè
- Infection and Cystic Fibrosis Unit, Istituto di Ricovero e Cura a Carattere Scientifico-San Raffaele Scientific Institute, Milan 20132, Italy
| | - Cristina Cigana
- Infection and Cystic Fibrosis Unit, Istituto di Ricovero e Cura a Carattere Scientifico-San Raffaele Scientific Institute, Milan 20132, Italy
| | | | | | - Mohamad A Hamad
- Department of Microbiology and Immunology, University of Western Ontario, London N6A 5C1, Canada
| | - Anthony De Soyza
- Applied Immunobiology and Transplantation Group, Institute of Cellular Medicine, University of Newcastle, Newcastle NE1 7RU, United Kingdom, and
| | - Alba Silipo
- From the Departments of Chemical Sciences and
| | - Roman Jerala
- Department of Biotechnology, National Institute of Chemistry, Ljubljana 1000, Slovenia, Centre of Excellence NMR - Future Innovation for Sustainable Technologies, Ljubljana 1000, Slovenia
| | - Alessandra Bragonzi
- Infection and Cystic Fibrosis Unit, Istituto di Ricovero e Cura a Carattere Scientifico-San Raffaele Scientific Institute, Milan 20132, Italy
| | - Miguel A Valvano
- Department of Microbiology and Immunology, University of Western Ontario, London N6A 5C1, Canada, Centre for Infection and Immunity, Queen's University Belfast, Belfast BT9 7AE, United Kingdom
| | - Sonsoles Martín-Santamaría
- Department of Chemistry and Biochemistry, Universidad CEU San Pablo, Boadilla del Monte, Madrid 28668, Spain,
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81
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Abstract
![]()
The
high mutation rate of the human immunodeficiency virus type
1 (HIV-1) virus is a major problem since it evades the function of
antibodies and chemical inhibitors. Here, we demonstrate a viral detection
strategy based on synthetic biology principles to detect a specific
viral function rather than a particular viral protein. The resistance
caused by mutations can be circumvented since the mutations that cause
the loss of function also incapacitate the virus. Many pathogens encode
proteases that are essential for their replication and that have a
defined substrate specificity. A genetically encoded sensor composed
of a fused membrane anchor, viral protease target site, and an orthogonal
transcriptional activator was engineered into a human cell line. The
HIV-1 protease released the transcriptional activator from the membrane,
thereby inducing transcription of the selected genes. The device was
still strongly activated by clinically relevant protease mutants that
are resistant to protease inhibitors. In the future, a similar principle
could be applied to detect also other pathogens and functions.
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Affiliation(s)
- Andreja Majerle
- Laboratory
of Biotechnology, National Institute of Chemistry, Hajdrihova
19, 1000 Ljubljana, Slovenia
| | - Rok Gaber
- Laboratory
of Biotechnology, National Institute of Chemistry, Hajdrihova
19, 1000 Ljubljana, Slovenia
| | - Mojca Benčina
- Laboratory
of Biotechnology, National Institute of Chemistry, Hajdrihova
19, 1000 Ljubljana, Slovenia
| | - Roman Jerala
- Laboratory
of Biotechnology, National Institute of Chemistry, Hajdrihova
19, 1000 Ljubljana, Slovenia
- EN-FIST Centre
of Excellence, Trg OF 13, 1000 Ljubljana, Slovenia
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82
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Manček-Keber M, Frank-Bertoncelj M, Hafner-Bratkovič I, Smole A, Zorko M, Pirher N, Hayer S, Kralj-Iglič V, Rozman B, Ilc N, Horvat S, Jerala R. Toll-like receptor 4 senses oxidative stress mediated by the oxidation of phospholipids in extracellular vesicles. Sci Signal 2015; 8:ra60. [PMID: 26082436 DOI: 10.1126/scisignal.2005860] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Oxidative stress produced in response to infection or sterile injury activates the innate immune response. We found that extracellular vesicles (EVs) isolated from the plasma of patients with rheumatoid arthritis or secreted from cells subjected to oxidative stress contained oxidized phospholipids that stimulated cells expressing Toll-like receptor 4 (TLR4) in a manner dependent on its co-receptor MD-2. EVs from healthy subjects or reconstituted synthetic EVs subjected to limited oxidation gained the ability to stimulate TLR4-expressing cells, whereas prolonged oxidation abrogated this property. Furthermore, we found that 15-lipoxygenase generated hydro(pero)xylated phospholipids that stimulated TLR4-expressing cells. Molecular modeling suggested that the mechanism of activation of TLR4 by oxidized phospholipids in EVs was structurally similar to that of the TLR4 ligand lipopolysaccharide (LPS). This was supported by experiments showing that EV-mediated stimulation of cells required MD-2, that mutations that block LPS binding to TLR4 abrogated the stimulatory effect of EVs, and that EVs induced TLR4 dimerization. On the other hand, analysis of gene expression profiles showed that genes encoding factors that resolve inflammation were more abundantly expressed in responses to EVs than in response to LPS. Together, these data suggest that EVs act as an oxidative stress-induced endogenous danger signal that underlies the pervasive role of TLR4 in inflammatory diseases.
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Affiliation(s)
- Mateja Manček-Keber
- Department of Biotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia. Excellent NMR Future Innovation for Sustainable Technologies, Centre of Excellence, 1000 Ljubljana, Slovenia.
| | - Mojca Frank-Bertoncelj
- Department of Rheumatology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Iva Hafner-Bratkovič
- Department of Biotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia. Excellent NMR Future Innovation for Sustainable Technologies, Centre of Excellence, 1000 Ljubljana, Slovenia
| | - Anže Smole
- Department of Biotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Mateja Zorko
- Department of Biotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Nina Pirher
- Department of Biotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Silvia Hayer
- Division of Rheumatology, Department of Internal Medicine III, Medical University of Vienna, 1090 Vienna, Austria
| | - Veronika Kralj-Iglič
- Laboratoryof Clinical Biophysics, Faculty of Health Sciences, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Blaž Rozman
- Department of Rheumatology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Nejc Ilc
- Faculty of Computer and Information Science, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Simon Horvat
- Department of Biotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia. Department of Animal Science, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Roman Jerala
- Department of Biotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia. Excellent NMR Future Innovation for Sustainable Technologies, Centre of Excellence, 1000 Ljubljana, Slovenia.
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83
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Jerala R. Structural and Functional Features of Recognition by Toll‐Like Receptors. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.718.2] [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: 11/11/2022]
Affiliation(s)
- Roman Jerala
- Biotechnology National institute of chemistryLjubljanaSlovenia
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84
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Abstract
Recent findings unexpectedly revealed that human TLR4 can be directly activated by nickel ions. This activation is due to the coordination of nickel by a cluster of histidine residues on the ectodomain of human TLR4, which is absent in most other species. We aimed to elucidate the role of MD-2 in the molecular mechanism of TLR4/MD-2 activation by nickel, as nickel binding site on TLR4 is remote from MD-2, which directly binds the endotoxin as the main pathological activator of TLR4. We identified MD-2 and TLR4 mutants which abolished TLR4/MD-2 receptor activation by endotoxin but could nevertheless be significantly activated by nickel, which acts in synergy with LPS. Human TLR4/MD-2 was also activated by cobalt ions, while copper and cadmium were toxic in the tested concentration range. Activation of TLR4 by cobalt required MD-2 and was abolished by human TLR4 mutations of histidine residues at positions 456 and 458. We demonstrated that activation of TLR4 by nickel and cobalt ions can trigger both the MyD88-dependent and the -independent pathway. Based on our results we propose that predominantly hydrophobic interactions between MD-2 and TLR4 contribute to the stabilization of the TLR4/MD-2/metal ion complex in a conformation that enables activation.
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Affiliation(s)
- Alja Oblak
- Department of Biotechnology, National institute of Chemistry, Ljubljana, Slovenia
- Centre of Excellence EN-FIST, Ljubljana, Slovenia
| | - Jelka Pohar
- Department of Biotechnology, National institute of Chemistry, Ljubljana, Slovenia
- Centre of Excellence EN-FIST, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Biotechnology, National institute of Chemistry, Ljubljana, Slovenia
- Centre of Excellence EN-FIST, Ljubljana, Slovenia
- * E-mail:
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85
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Pohar J, Kužnik Krajnik A, Jerala R, Benčina M. Minimal sequence requirements for oligodeoxyribonucleotides activating human TLR9. J Immunol 2015; 194:3901-8. [PMID: 25780037 DOI: 10.4049/jimmunol.1402755] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 02/08/2015] [Indexed: 11/19/2022]
Abstract
Synthetic oligodeoxyribonucleotides (ODNs) containing CpG (unmethylated deoxycytidylyl-deoxyguanosine dinucleotide) motifs activate endosomal TLR9. The nucleotide sequence, length, and dimerization properties of ODNs modulate their activation of TLR9. We performed a systematic investigation of the sequence motifs of B-class and C-class phosphodiester ODNs to identify the sequence properties that govern TLR9 activation. ODNs shorter than 21 nt and with the adenosine adjacent to the cytidine-guanosine (CG) dinucleotide motif led to a significant loss of the propensity to activate TLR9. The distance between the stimulatory CpG motifs within the ODN fine-tunes the activation of B cells. The minimal ODNs that activate human TLR9 comprise 2 CG dinucleotides separated by 6-10 nt, where the first CpG motif is preceded by the 5'-thymidine and the elongated poly-thymidine tail at the 3' end of the ODN. The minimal sequence provides insight into the molecular mechanism of TLR9 ligand recognition. On the basis of sequence requirements, we conclude that two binding sites with different affinities for CG are formed in the human TLR9 dimer, with a very stringent binding site interacting with the 5' CpG motif.
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Affiliation(s)
- Jelka Pohar
- Department of Biotechnology, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia; and
| | - Alenka Kužnik Krajnik
- Department of Biotechnology, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia; and
| | - Roman Jerala
- Department of Biotechnology, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia; and EN-FIST Centre of Excellence, SI-1000 Ljubljana, Slovenia
| | - Mojca Benčina
- Department of Biotechnology, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia; and EN-FIST Centre of Excellence, SI-1000 Ljubljana, Slovenia
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86
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Manček-Keber M, Jerala R. Postulates for validating TLR4 agonists. Eur J Immunol 2015; 45:356-70. [DOI: 10.1002/eji.201444462] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 10/20/2014] [Accepted: 12/01/2014] [Indexed: 02/03/2023]
Affiliation(s)
- Mateja Manček-Keber
- Department of Biotechnology; National Institute of Chemistry; Ljubljana Slovenia
- EN-FIST Centre of Excellence; Ljubljana Slovenia
| | - Roman Jerala
- Department of Biotechnology; National Institute of Chemistry; Ljubljana Slovenia
- EN-FIST Centre of Excellence; Ljubljana Slovenia
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87
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Molinaro A, Holst O, Di Lorenzo F, Callaghan M, Nurisso A, D'Errico G, Zamyatina A, Peri F, Berisio R, Jerala R, Jiménez-Barbero J, Silipo A, Martín-Santamaría S. Cover Picture: Chemistry of Lipid A: At the Heart of Innate Immunity (Chem. Eur. J. 2/2015). Chemistry 2015. [DOI: 10.1002/chem.201590000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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88
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Hadži S, Ondračka A, Jerala R, Hafner‐Bratkovič I. Pathological mutations H187R and E196K facilitate subdomain separation and prion protein conversion by destabilization of the native structure. FASEB J 2014; 29:882-93. [DOI: 10.1096/fj.14-255646] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- San Hadži
- Department of BiotechnologyNational Institute of ChemistryLjubljanaSlovenia
| | - Andrej Ondračka
- Department of BiotechnologyNational Institute of ChemistryLjubljanaSlovenia
| | - Roman Jerala
- Department of BiotechnologyNational Institute of ChemistryLjubljanaSlovenia
- EN‐FIST Centre of ExcellenceLjubljanaSlovenia
| | - Iva Hafner‐Bratkovič
- Department of BiotechnologyNational Institute of ChemistryLjubljanaSlovenia
- EN‐FIST Centre of ExcellenceLjubljanaSlovenia
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89
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Molinaro A, Holst O, Di Lorenzo F, Callaghan M, Nurisso A, D'Errico G, Zamyatina A, Peri F, Berisio R, Jerala R, Jiménez-Barbero J, Silipo A, Martín-Santamaría S. Chemistry of Lipid A: At the Heart of Innate Immunity. Chemistry 2014. [DOI: 10.1002/chem.201405771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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90
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Molinaro A, Holst O, Di Lorenzo F, Callaghan M, Nurisso A, D'Errico G, Zamyatina A, Peri F, Berisio R, Jerala R, Jiménez-Barbero J, Silipo A, Martín-Santamaría S. Chemistry of lipid A: at the heart of innate immunity. Chemistry 2014; 21:500-19. [PMID: 25353096 DOI: 10.1002/chem.201403923] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In many Gram-negative bacteria, lipopolysaccharide (LPS) and its lipid A moiety are pivotal for bacterial survival. Depending on its structure, lipid A carries the toxic properties of the LPS and acts as a potent elicitor of the host innate immune system via the Toll-like receptor 4/myeloid differentiation factor 2 (TLR4/MD-2) receptor complex. It often causes a wide variety of biological effects ranging from a remarkable enhancement of the resistance to the infection to an uncontrolled and massive immune response resulting in sepsis and septic shock. Since the bioactivity of lipid A is strongly influenced by its primary structure, a broad range of chemical syntheses of lipid A derivatives have made an enormous contribution to the characterization of lipid A bioactivity, providing novel pharmacological targets for the development of new biomedical therapies. Here, we describe and discuss the chemical aspects regarding lipid A and its role in innate immunity, from the (bio)synthesis, isolation and characterization to the molecular recognition at the atomic level.
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Affiliation(s)
- Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II via Cinthia 4, 80126 Napoli (Italy).
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91
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Rodriguez Lavado J, Sestito SE, Cighetti R, Aguilar Moncayo EM, Oblak A, Lainšček D, Jiménez Blanco JL, García Fernández JM, Ortiz Mellet C, Jerala R, Calabrese V, Peri F. Trehalose- and glucose-derived glycoamphiphiles: small-molecule and nanoparticle Toll-like receptor 4 (TLR4) modulators. J Med Chem 2014; 57:9105-23. [PMID: 25268544 DOI: 10.1021/jm501182w] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
An increasing number of pathologies have been linked to Toll-like receptor 4 (TLR4) activation and signaling, therefore new hit and lead compounds targeting this receptor activation process are urgently needed. We report on the synthesis and biological properties of glycolipids based on glucose and trehalose scaffolds which potently inhibit TLR4 activation and signaling in vitro and in vivo. Structure-activity relationship studies on these compounds indicate that the presence of fatty ester chains in the molecule is a primary prerequisite for biological activity and point to facial amphiphilicity as a preferred architecture for TLR4 antagonism. The cationic glycolipids here presented can be considered as new lead compounds for the development of drugs targeting TLR4 activation and signaling in infectious, inflammatory, and autoimmune diseases. Interestingly, the biological activity of the best drug candidate was retained after adsorption at the surface of colloidal gold nanoparticles, broadening the options for clinical development.
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Affiliation(s)
- Julio Rodriguez Lavado
- Department of Organic Chemistry, Faculty of Chemistry, University of Sevilla , E-41012 Sevilla, Spain
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92
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Lebar T, Bezeljak U, Golob A, Jerala M, Kadunc L, Pirš B, Stražar M, Vučko D, Zupančič U, Benčina M, Forstnerič V, Gaber R, Lonzarić J, Majerle A, Oblak A, Smole A, Jerala R. A bistable genetic switch based on designable DNA-binding domains. Nat Commun 2014; 5:5007. [PMID: 25264186 DOI: 10.1038/ncomms6007] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 08/15/2014] [Indexed: 12/31/2022] Open
Abstract
Bistable switches are fundamental regulatory elements of complex systems, ranging from electronics to living cells. Designed genetic toggle switches have been constructed from pairs of natural transcriptional repressors wired to inhibit one another. The complexity of the engineered regulatory circuits can be increased using orthogonal transcriptional regulators based on designed DNA-binding domains. However, a mutual repressor-based toggle switch comprising DNA-binding domains of transcription-activator-like effectors (TALEs) did not support bistability in mammalian cells. Here, the challenge of engineering a bistable switch based on monomeric DNA-binding domains is solved via the introduction of a positive feedback loop composed of activators based on the same TALE domains as their opposing repressors and competition for the same DNA operator site. This design introduces nonlinearity and results in epigenetic bistability. This principle could be used to employ other monomeric DNA-binding domains such as CRISPR for applications ranging from reprogramming cells to building digital biological memory.
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Affiliation(s)
- Tina Lebar
- 1] Department of Biotechnology, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia [2] EN-FIST Centre of Excellence, Ljubljana 1000, Slovenia
| | - Urban Bezeljak
- Slovenian iGEM Team 2012, National Institute of Chemistry and University of Ljubljana, Ljubljana 1000, Slovenia
| | - Anja Golob
- 1] Department of Biotechnology, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia [2] Slovenian iGEM Team 2012, National Institute of Chemistry and University of Ljubljana, Ljubljana 1000, Slovenia
| | - Miha Jerala
- Slovenian iGEM Team 2012, National Institute of Chemistry and University of Ljubljana, Ljubljana 1000, Slovenia
| | - Lucija Kadunc
- 1] Department of Biotechnology, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia [2] Slovenian iGEM Team 2012, National Institute of Chemistry and University of Ljubljana, Ljubljana 1000, Slovenia
| | - Boštjan Pirš
- Slovenian iGEM Team 2012, National Institute of Chemistry and University of Ljubljana, Ljubljana 1000, Slovenia
| | - Martin Stražar
- 1] Slovenian iGEM Team 2012, National Institute of Chemistry and University of Ljubljana, Ljubljana 1000, Slovenia [2] Faculty of Computer and Information Science, University of Ljubljana, Večna pot 113, Ljubljana 1000, Slovenia
| | - Dušan Vučko
- Slovenian iGEM Team 2012, National Institute of Chemistry and University of Ljubljana, Ljubljana 1000, Slovenia
| | - Uroš Zupančič
- Slovenian iGEM Team 2012, National Institute of Chemistry and University of Ljubljana, Ljubljana 1000, Slovenia
| | - Mojca Benčina
- 1] Department of Biotechnology, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia [2] EN-FIST Centre of Excellence, Ljubljana 1000, Slovenia
| | - Vida Forstnerič
- Department of Biotechnology, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia
| | - Rok Gaber
- 1] Department of Biotechnology, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia [2] EN-FIST Centre of Excellence, Ljubljana 1000, Slovenia
| | - Jan Lonzarić
- 1] Department of Biotechnology, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia [2] EN-FIST Centre of Excellence, Ljubljana 1000, Slovenia
| | - Andreja Majerle
- 1] Department of Biotechnology, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia [2] EN-FIST Centre of Excellence, Ljubljana 1000, Slovenia
| | - Alja Oblak
- 1] Department of Biotechnology, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia [2] EN-FIST Centre of Excellence, Ljubljana 1000, Slovenia
| | - Anže Smole
- Department of Biotechnology, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia
| | - Roman Jerala
- 1] Department of Biotechnology, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia [2] EN-FIST Centre of Excellence, Ljubljana 1000, Slovenia
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93
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Adanitsch F, Ittig S, Stöckl J, Oblak A, Haegman M, Jerala R, Beyaert R, Kosma P, Zamyatina A. Development of αGlcN(1↔1)αMan-based lipid A mimetics as a novel class of potent Toll-like receptor 4 agonists. J Med Chem 2014; 57:8056-71. [PMID: 25252784 PMCID: PMC4191062 DOI: 10.1021/jm500946r] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
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The endotoxic portion of lipopolysaccharide
(LPS), a glycophospholipid
Lipid A, initiates the activation of the Toll-like Receptor 4 (TLR4)–myeloid
differentiation factor 2 (MD-2) complex, which results in pro-inflammatory
immune signaling. To unveil the structural requirements for TLR4·MD-2-specific
ligands, we have developed conformationally restricted Lipid A mimetics
wherein the flexible βGlcN(1→6)GlcN backbone of Lipid
A is exchanged for a rigid trehalose-like αGlcN(1↔1)αMan scaffold
resembling the molecular shape of TLR4·MD-2-bound E.
coli Lipid A disclosed in the X-ray structure. A convergent
synthetic route toward orthogonally protected αGlcN(1↔1)αMan
disaccharide has been elaborated. The α,α-(1↔1)
linkage was attained by the glycosylation of 2-N-carbamate-protected
α-GlcN-lactol with N-phenyl-trifluoroacetimidate
of 2-O-methylated mannose. Regioselective acylation
with (R)-3-acyloxyacyl fatty acids and successive
phosphorylation followed by global deprotection afforded bis- and
monophosphorylated hexaacylated Lipid A mimetics. αGlcN(1↔1)αMan-based
Lipid A mimetics (α,α-GM-LAM) induced potent activation
of NF-κB signaling in hTLR4/hMD-2/CD14-transfected HEK293 cells
and robust LPS-like cytokines expression in macrophages and dendritic
cells. Thus, restricting the conformational flexibility of Lipid A
by fixing the molecular shape of its carbohydrate backbone in the
“agonistic” conformation attained by a rigid αGlcN(1↔1)αMan scaffold
represents
an efficient approach toward powerful and adjustable TLR4 activation.
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Affiliation(s)
- Florian Adanitsch
- Department of Chemistry, University of Natural Resources and Life Sciences , Muthgasse 18, A-1190 Vienna, Austria
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94
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Kočar V, Božič Abram S, Doles T, Bašić N, Gradišar H, Pisanski T, Jerala R. TOPOFOLD, the designed modular biomolecular folds: polypeptide-based molecular origami nanostructures following the footsteps of DNA. Wiley Interdiscip Rev Nanomed Nanobiotechnol 2014; 7:218-37. [PMID: 25196147 DOI: 10.1002/wnan.1289] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Revised: 07/08/2014] [Accepted: 07/20/2014] [Indexed: 12/14/2022]
Abstract
Biopolymers, the essential components of life, are able to form many complex nanostructures, and proteins in particular are the material of choice for most cellular processes. Owing to numerous cooperative interactions, rational design of new protein folds remains extremely challenging. An alternative strategy is to design topofolds-nanostructures built from polypeptide arrays of interacting modules that define their topology. Over the course of the last several decades DNA has successfully been repurposed from its native role of information storage to a smart nanomaterial used for nanostructure self-assembly of almost any shape, which is largely because of its programmable nature. Unfortunately, polypeptides do not possess the straightforward complementarity as do nucleic acids. However, a modular approach can nevertheless be used to assemble polypeptide nanostructures, as was recently demonstrated on a single-chain polypeptide tetrahedron. This review focuses on the current state-of-the-art in the field of topological polypeptide folds. It starts with a brief overview of the field of structural DNA and RNA nanotechnology, from which it draws parallels and possible directions of development for the emerging field of polypeptide-based nanotechnology. The principles of topofold strategy and unique properties of such polypeptide nanostructures in comparison to native protein folds are discussed. Reasons for the apparent absence of such folds in nature are also examined. Physicochemical versatility of amino acid residues and cost-effective production makes polypeptides an attractive platform for designed functional bionanomaterials.
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Affiliation(s)
- Vid Kočar
- Department of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia
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95
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Zweytick D, Japelj B, Mileykovskaya E, Zorko M, Dowhan W, Blondelle SE, Riedl S, Jerala R, Lohner K. N-acylated peptides derived from human lactoferricin perturb organization of cardiolipin and phosphatidylethanolamine in cell membranes and induce defects in Escherichia coli cell division. PLoS One 2014; 9:e90228. [PMID: 24595074 PMCID: PMC3940911 DOI: 10.1371/journal.pone.0090228] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 01/31/2014] [Indexed: 11/18/2022] Open
Abstract
Two types of recently described antibacterial peptides derived from human lactoferricin, either nonacylated or N-acylated, were studied for their different interaction with membranes of Escherichia coli in vivo and in model systems. Electron microscopy revealed striking effects on the bacterial membrane as both peptide types induced formation of large membrane blebs. Electron and fluorescence microscopy, however demonstrated that only the N-acylated peptides partially induced the generation of oversized cells, which might reflect defects in cell-division. Further a different distribution of cardiolipin domains on the E. coli membrane was shown only in the presence of the N-acylated peptides. The lipid was distributed over the whole bacterial cell surface, whereas cardiolipin in untreated and nonacylated peptide-treated cells was mainly located at the septum and poles. Studies with bacterial membrane mimics, such as cardiolipin or phosphatidylethanolamine revealed that both types of peptides interacted with the negatively charged lipid cardiolipin. The nonacylated peptides however induced segregation of cardiolipin into peptide-enriched and peptide-poor lipid domains, while the N-acylated peptides promoted formation of many small heterogeneous domains. Only N-acylated peptides caused additional severe effects on the main phase transition of liposomes composed of pure phosphatidylethanolamine, while both peptide types inhibited the lamellar to hexagonal phase transition. Lipid mixtures of phosphatidylethanolamine and cardiolipin revealed anionic clustering by all peptide types. However additional strong perturbation of the neutral lipids was only seen with the N-acylated peptides. Nuclear magnetic resonance demonstrated different conformational arrangement of the N-acylated peptide in anionic and zwitterionic micelles revealing possible mechanistic differences in their action on different membrane lipids. We hypothesized that both peptides kill bacteria by interacting with bacterial membrane lipids but only N-acylated peptides interact with both charged cardiolipin and zwitterionic phosphatidylethanolamine resulting in remodeling of the natural phospholipid domains in the E. coli membrane that leads to defects in cell division.
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Affiliation(s)
- Dagmar Zweytick
- Institute of Molecular Biosciences, Biophysics Division, University of Graz, Graz, Austria
- * E-mail:
| | - Bostjan Japelj
- Department of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Eugenia Mileykovskaya
- Department of Biochemistry and Molecular Biology, University of Texas Medical School-Houston, Houston, Texas, United States of America
| | - Mateja Zorko
- Department of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - William Dowhan
- Department of Biochemistry and Molecular Biology, University of Texas Medical School-Houston, Houston, Texas, United States of America
| | - Sylvie E. Blondelle
- Department of Biochemistry, Torrey Pines Institute for Molecular Studies, San Diego, California, United States of America
| | - Sabrina Riedl
- Institute of Molecular Biosciences, Biophysics Division, University of Graz, Graz, Austria
| | - Roman Jerala
- Department of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia
- Centre of Excellence EN-FIST, Ljubljana, Slovenia
| | - Karl Lohner
- Institute of Molecular Biosciences, Biophysics Division, University of Graz, Graz, Austria
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96
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Abstract
Natural polymers are able to self-assemble into versatile nanostructures based on the information encoded into their primary structure. The structural richness of biopolymer-based nanostructures depends on the information content of building blocks and the available biological machinery to assemble and decode polymers with a defined sequence. Natural polypeptides comprise 20 amino acids with very different properties in comparison to only 4 structurally similar nucleotides, building elements of nucleic acids. Nevertheless the ease of synthesizing polynucleotides with selected sequence and the ability to encode the nanostructural assembly based on the two specific nucleotide pairs underlay the development of techniques to self-assemble almost any selected three-dimensional nanostructure from polynucleotides. Despite more complex design rules, peptides were successfully used to assemble symmetric nanostructures, such as fibrils and spheres. While earlier designed protein-based nanostructures used linked natural oligomerizing domains, recent design of new oligomerizing interaction surfaces and introduction of the platform for topologically designed protein fold may enable polypeptide-based design to follow the track of DNA nanostructures. The advantages of protein-based nanostructures, such as the functional versatility and cost effective and sustainable production methods provide strong incentive for further development in this direction.
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Affiliation(s)
- Helena Gradišar
- Department of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia
- Excellent NMR – Future Innovation for Sustainable Technologies, Centre of Excellence, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia
- Excellent NMR – Future Innovation for Sustainable Technologies, Centre of Excellence, Ljubljana, Slovenia
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97
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Resman N, Oblak A, Gioannini TL, Weiss JP, Jerala R. Tetraacylated lipid A and paclitaxel-selective activation of TLR4/MD-2 conferred through hydrophobic interactions. J Immunol 2014; 192:1887-95. [PMID: 24420921 DOI: 10.4049/jimmunol.1302119] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
LPS exerts potent immunostimulatory effects through activation of the TLR4/MD-2 receptor complex. The hexaacylated lipid A is an agonist of mouse (mTLR4) and human TLR4/MD-2, whereas the tetraacylated lipid IVa and paclitaxel activate only mTLR4/MD-2 and antagonize activation of the human receptor complex. Hydrophobic mutants of TLR4 or MD-2 were used to investigate activation of human embryonic kidney 293 cells by different TLR4 agonists. We show that each of the hydrophobic residues F438 and F461, which are located on the convex face of leucine-rich repeats 16 and 17 of the mTLR4 ectodomain, are essential for activation of with lipid IVa and paclitaxel, which, although not a structural analog of LPS, activates cells expressing mTLR4/MD-2. Both TLR4 mutants were inactive when stimulated with lipid IVa or paclitaxel, but retained significant activation when stimulated with LPS or hexaacylated lipid A. We show that the phenylalanine residue at position 126 of mouse MD-2 is indispensable only for activation with paclitaxel. Its replacement with leucine or valine completely abolished activation with paclitaxel while preserving the responsiveness to lipid IVa and lipid A. This suggests specific interaction of paclitaxel with F126 because its replacement with leucine even augmented activation by lipid A. These results provide an insight into the molecular mechanism of TLR4 activation by two structurally very different agonists.
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Affiliation(s)
- Nusa Resman
- Department of Biotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
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98
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Gaber R, Lebar T, Majerle A, Šter B, Dobnikar A, Benčina M, Jerala R. Designable DNA-binding domains enable construction of logic circuits in mammalian cells. Nat Chem Biol 2014; 10:203-8. [PMID: 24413461 DOI: 10.1038/nchembio.1433] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 11/19/2013] [Indexed: 11/09/2022]
Abstract
Electronic computer circuits consisting of a large number of connected logic gates of the same type, such as NOR, can be easily fabricated and can implement any logic function. In contrast, designed genetic circuits must employ orthogonal information mediators owing to free diffusion within the cell. Combinatorial diversity and orthogonality can be provided by designable DNA- binding domains. Here, we employed the transcription activator-like repressors to optimize the construction of orthogonal functionally complete NOR gates to construct logic circuits. We used transient transfection to implement all 16 two-input logic functions from combinations of the same type of NOR gates within mammalian cells. Additionally, we present a genetic logic circuit where one input is used to select between an AND and OR function to process the data input using the same circuit. This demonstrates the potential of designable modular transcription factors for the construction of complex biological information-processing devices.
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Affiliation(s)
- Rok Gaber
- 1] Department of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia. [2] EN-FIST Centre of Excellence, Ljubljana, Slovenia. [3]
| | - Tina Lebar
- 1] Department of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia. [2] EN-FIST Centre of Excellence, Ljubljana, Slovenia. [3]
| | - Andreja Majerle
- 1] Department of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia. [2] EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Branko Šter
- Faculty of Computer and Information Science, University of Ljubljana, Slovenia
| | - Andrej Dobnikar
- Faculty of Computer and Information Science, University of Ljubljana, Slovenia
| | - Mojca Benčina
- 1] Department of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia. [2] EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Roman Jerala
- 1] Department of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia. [2] EN-FIST Centre of Excellence, Ljubljana, Slovenia
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99
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Cighetti R, Ciaramelli C, Sestito SE, Zanoni I, Kubik Ł, Ardá-Freire A, Calabrese V, Granucci F, Jerala R, Martín-Santamaría S, Jiménez-Barbero J, Peri F. Modulation of CD14 and TLR4·MD-2 activities by a synthetic lipid A mimetic. Chembiochem 2013; 15:250-8. [PMID: 24339336 DOI: 10.1002/cbic.201300588] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [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: 09/13/2013] [Indexed: 12/13/2022]
Abstract
Monosaccharide lipid A mimetics based on a glucosamine core linked to two fatty acid chains and bearing one or two phosphate groups have been synthesized. Compounds 1 and 2, each with one phosphate group, were practically inactive in inhibiting LPS-induced TLR4 signaling and cytokine production in HEK-blue cells and murine macrophages, but compound 3, with two phosphate groups, was found to be active in efficiently inhibiting TLR4 signal in both cell types. The direct interaction between compound 3 and the MD-2 coreceptor was investigated by NMR spectroscopy and molecular modeling/docking analysis. This compound also interacts directly with the CD14 receptor, stimulating its internalization by endocytosis. Experiments on macrophages show that the effect on CD14 reinforces the activity on MD-2·TLR4 because compound 3's activity is higher when CD14 is important for TLR4 signaling (i.e., at low LPS concentration). The dual targeting of MD-2 and CD14, accompanied by good solubility in water and lack of toxicity, suggests the use of monosaccharide 3 as a lead compound for the development of drugs directed against TLR4-related syndromes.
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Affiliation(s)
- Roberto Cighetti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy)
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100
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Gaber R, Majerle A, Jerala R, Benčina M. Noninvasive high-throughput single-cell analysis of HIV protease activity using ratiometric flow cytometry. Sensors (Basel) 2013; 13:16330-46. [PMID: 24287545 PMCID: PMC3892856 DOI: 10.3390/s131216330] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 11/11/2013] [Accepted: 11/13/2013] [Indexed: 11/16/2022]
Abstract
To effectively fight against the human immunodeficiency virus infection/ acquired immunodeficiency syndrome (HIV/AIDS) epidemic, ongoing development of novel HIV protease inhibitors is required. Inexpensive high-throughput screening assays are needed to quickly scan large sets of chemicals for potential inhibitors. We have developed a Förster resonance energy transfer (FRET)-based, HIV protease-sensitive sensor using a combination of a fluorescent protein pair, namely mCerulean and mCitrine. Through extensive in vitro characterization, we show that the FRET-HIV sensor can be used in HIV protease screening assays. Furthermore, we have used the FRET-HIV sensor for intracellular quantitative detection of HIV protease activity in living cells, which more closely resembles an actual viral infection than an in vitro assay. We have developed a high-throughput method that employs a ratiometric flow cytometry for analyzing large populations of cells that express the FRET-HIV sensor. The method enables FRET measurement of single cells with high sensitivity and speed and should be used when subpopulation-specific intracellular activity of HIV protease needs to be estimated. In addition, we have used a confocal microscopy sensitized emission FRET technique to evaluate the usefulness of the FRET-HIV sensor for spatiotemporal detection of intracellular HIV protease activity.
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Affiliation(s)
- Rok Gaber
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana 1000, Slovenia; E-Mails: (R.G.); (A.M.); (R.J.)
- Center of Excellence EN-FIST, Ljubljana 1000, Slovenia
| | - Andreja Majerle
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana 1000, Slovenia; E-Mails: (R.G.); (A.M.); (R.J.)
- Center of Excellence EN-FIST, Ljubljana 1000, Slovenia
| | - Roman Jerala
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana 1000, Slovenia; E-Mails: (R.G.); (A.M.); (R.J.)
- Center of Excellence EN-FIST, Ljubljana 1000, Slovenia
| | - Mojca Benčina
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana 1000, Slovenia; E-Mails: (R.G.); (A.M.); (R.J.)
- Center of Excellence EN-FIST, Ljubljana 1000, Slovenia
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +386-1-4760-334; Fax: +386-1-4760-300
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