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Lukasak B, Thompson RE, Mitchener MM, Feng VJ, Bagert JD, Muir TW. A Genetically Encoded Approach for Breaking Chromatin Symmetry. ACS CENTRAL SCIENCE 2022; 8:176-183. [PMID: 35233450 PMCID: PMC8875426 DOI: 10.1021/acscentsci.1c01332] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Indexed: 05/03/2023]
Abstract
Nucleosomes frequently exist as asymmetric species in native chromatin contexts. Current methods for the traceless generation of these heterotypic chromatin substrates are inefficient and/or difficult to implement. Here, we report an application of the SpyCatcher/SpyTag system as a convenient route to assemble desymmetrized nucleoprotein complexes. This genetically encoded covalent tethering system serves as an internal chaperone, maintained through the assembly process, affording traceless asymmetric nucleosomes following proteolytic removal of the tethers. The strategy allows for generation of nucleosomes containing asymmetric modifications on single or multiple histones, thereby providing facile access to a range of substrates. Herein, we use such constructs to interrogate how nucleosome desymmetrization caused by the incorporation of cancer-associated histone mutations alters chromatin remodeling processes. We also establish that our system provides access to asymmetric dinucleosomes, which allowed us to query the geometric/symmetry constraints of the unmodified histone H3 tail in stimulating the activity of the histone lysine demethylase, KDM5B. By providing a streamlined approach to generate these sophisticated substrates, our method expands the chemical biology toolbox available for interrogating the consequences of asymmetry on chromatin structure and function.
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102
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Schindler C, Faust C, Sjuts H, Lange C, Kühn J, Dittrich W, Leuschner WD, Schiebler W, Hofmann J, Rao E, Langer T. A multivalent antibody assembled from different building blocks using tag/catcher systems: a case study. Protein Eng Des Sel 2022; 35:6826492. [PMID: 36373216 DOI: 10.1093/protein/gzac014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
The field of therapeutic antibodies and, especially bi- or multispecific antibodies, is growing rapidly. Especially for treating cancers, multispecific antibodies are very promising, as there are multiple pathways involved and multispecific antibodies offer the possibility to interfere at two or more sites. Besides being used as therapeutic, multispecific antibodies can be helpful tools in basic research. However, the design and choice of the most appropriate multispecific antibody format are far from trivial. The generation of multispecific antibodies starts with the generation of antibodies directed against the desired targets and then combining the different antigen-binding sites in one molecule. This is a time-consuming and laborious approach since the most suitable geometry cannot be predicted. The SpyTag technology is based on a split-protein system, where a small peptide of said protein, the SpyTag, can bind to the remaining protein, the SpyCatcher. An irreversible isopeptide bond between the SpyTag and the SpyCatcher is formed. A related Tag-Catcher system is the SnoopTag-SnoopCatcher. These systems offer the opportunity to separately produce proteins fused to the tag-peptides and to the catcher-domains and assemble them in vitro. Our goal was to design and produce different antibody fragments, Fab domains and Fc-containing domains, with different tags and/or catchers as building blocks for the assembly of different multivalent antibodies. We have shown that large multivalent antibodies consisting of up to seven building blocks can be prepared. Binding experiments demonstrated that all binding sites in such a large molecule retained their accessibility to their corresponding antigens.
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Affiliation(s)
- Christof Schindler
- Sanofi-Aventis Deutschland GmbH, R&D Large Molecules Research, Industriepark Höchst, Frankfurt am Main 65926, Germany.,Lonza AG, QC Biologics, Lonzastraße, 3930 Visp, Switzerland
| | - Christine Faust
- Sanofi-Aventis Deutschland GmbH, R&D Large Molecules Research, Industriepark Höchst, Frankfurt am Main 65926, Germany
| | - Hanno Sjuts
- Sanofi-Aventis Deutschland GmbH, R&D Large Molecules Research, Industriepark Höchst, Frankfurt am Main 65926, Germany
| | - Christian Lange
- Sanofi-Aventis Deutschland GmbH, R&D Large Molecules Research, Industriepark Höchst, Frankfurt am Main 65926, Germany
| | - Jennifer Kühn
- Sanofi-Aventis Deutschland GmbH, R&D Large Molecules Research, Industriepark Höchst, Frankfurt am Main 65926, Germany
| | - Werner Dittrich
- Sanofi-Aventis Deutschland GmbH, R&D Large Molecules Research, Industriepark Höchst, Frankfurt am Main 65926, Germany
| | - Wulf Dirk Leuschner
- Sanofi-Aventis Deutschland GmbH, R&D Large Molecules Research, Industriepark Höchst, Frankfurt am Main 65926, Germany
| | - Werner Schiebler
- Provadis School of International Management and Technology AG, Industriepark Höchst, Building B845, Frankfurt am Main 65926, Germany
| | - Joachim Hofmann
- Provadis School of International Management and Technology AG, Industriepark Höchst, Building B845, Frankfurt am Main 65926, Germany
| | - Ercole Rao
- Sanofi-Aventis Deutschland GmbH, R&D Large Molecules Research, Industriepark Höchst, Frankfurt am Main 65926, Germany
| | - Thomas Langer
- Sanofi-Aventis Deutschland GmbH, R&D Large Molecules Research, Industriepark Höchst, Frankfurt am Main 65926, Germany
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103
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Gao Q, Ming D. Protein-protein interactions enhance the thermal resilience of SpyRing-cyclized enzymes: A molecular dynamic simulation study. PLoS One 2022; 17:e0263792. [PMID: 35176056 PMCID: PMC8853484 DOI: 10.1371/journal.pone.0263792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 01/26/2022] [Indexed: 12/02/2022] Open
Abstract
Recently a technique based on the interaction between adhesion proteins extracted from Streptococcus pyogenes, known as SpyRing, has been widely used to improve the thermal resilience of enzymes, the assembly of biostructures, cancer cell recognition and other fields. It was believed that the covalent cyclization of protein skeleton caused by SpyRing reduces the conformational entropy of biological structure and improves its rigidity, thus improving the thermal resilience of the target enzyme. However, the effects of SpyTag/ SpyCatcher interaction with this enzyme are poorly understood, and their regulation of enzyme properties remains unclear. Here, for simplicity, we took the single domain enzyme lichenase from Bacillus subtilis 168 as an example, studied the interface interactions in the SpyRing by molecular dynamics simulations, and examined the effects of the changes of electrostatic interaction and van der Waals interaction on the thermal resilience of target enzyme. The simulations showed that the interface between SpyTag/SpyCatcher and the target enzyme is different from that found by geometric matching method and highlighted key mutations at the interface that might have effect on the thermal resilience of the enzyme. Our calculations highlighted interfacial interactions between enzyme and SpyTag/SpyCatcher, which might be useful in rational designs of the SpyRing.
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Affiliation(s)
- Qi Gao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing City, Jiangsu, PR China
| | - Dangling Ming
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing City, Jiangsu, PR China
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104
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Protease-controlled secretion and display of intercellular signals. Nat Commun 2022; 13:912. [PMID: 35177637 PMCID: PMC8854555 DOI: 10.1038/s41467-022-28623-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/03/2022] [Indexed: 02/07/2023] Open
Abstract
To program intercellular communication for biomedicine, it is crucial to regulate the secretion and surface display of signaling proteins. If such regulations are at the protein level, there are additional advantages, including compact delivery and direct interactions with endogenous signaling pathways. Here we create a modular, generalizable design called Retained Endoplasmic Cleavable Secretion (RELEASE), with engineered proteins retained in the endoplasmic reticulum and displayed/secreted in response to specific proteases. The design allows functional regulation of multiple synthetic and natural proteins by synthetic protease circuits to realize diverse signal processing capabilities, including logic operation and threshold tuning. By linking RELEASE to additional sensing and processing circuits, we can achieve elevated protein secretion in response to "undruggable" oncogene KRAS mutants. RELEASE should enable the local, programmable delivery of intercellular cues for a broad variety of fields such as neurobiology, cancer immunotherapy and cell transplantation.
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105
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Sheikh A, Wangdi T, Vickers TJ, Aaron B, Palmer M, Miller MJ, Kim S, Herring C, Simoes R, Crainic JA, Gildersleeve JC, van der Post S, Hansson GC, Fleckenstein JM. Enterotoxigenic Escherichia coli Degrades the Host MUC2 Mucin Barrier To Facilitate Critical Pathogen-Enterocyte Interactions in Human Small Intestine. Infect Immun 2022; 90:e0057221. [PMID: 34807735 PMCID: PMC8853678 DOI: 10.1128/iai.00572-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/12/2021] [Indexed: 02/08/2023] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) isolates are genetically diverse pathological variants of E. coli defined by the production of heat-labile (LT) and/or heat-stable (ST) toxins. ETEC strains are estimated to cause hundreds of millions of cases of diarrheal illness annually. However, it is not clear that all strains are equally equipped to cause disease, and asymptomatic colonization with ETEC is common in low- to middle-income regions lacking basic sanitation and clean water where ETEC are ubiquitous. Recent molecular epidemiology studies have revealed a significant association between strains that produce EatA, a secreted autotransporter protein, and the development of symptomatic infection. Here, we demonstrate that LT stimulates production of MUC2 mucin by goblet cells in human small intestine, enhancing the protective barrier between pathogens and enterocytes. In contrast, using explants of human small intestine as well as small intestinal enteroids, we show that EatA counters this host defense by engaging and degrading the MUC2 mucin barrier to promote bacterial access to target enterocytes and ultimately toxin delivery, suggesting that EatA plays a crucial role in the molecular pathogenesis of ETEC. These findings may inform novel approaches to prevention of acute diarrheal illness as well as the sequelae associated with ETEC and other pathogens that rely on EatA and similar proteases for efficient interaction with their human hosts.
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Affiliation(s)
- Alaullah Sheikh
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Tamding Wangdi
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Tim J. Vickers
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Bailey Aaron
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Margot Palmer
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Mark J. Miller
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Seonyoung Kim
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Cassandra Herring
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Rita Simoes
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Jennifer A. Crainic
- Center for Cancer Research, Chemical Biology Laboratory, National Cancer Institute, Fredrick, Maryland, USA
| | - Jeffrey C. Gildersleeve
- Center for Cancer Research, Chemical Biology Laboratory, National Cancer Institute, Fredrick, Maryland, USA
| | - Sjoerd van der Post
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Gunnar C. Hansson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - James M. Fleckenstein
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, Saint Louis, Missouri, USA
- Medicine Service, Veterans Affairs Medical Center, Saint Louis, Missouri, USA
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106
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Tseng CY, Wang WX, Douglas TR, Chou LYT. Engineering DNA Nanostructures to Manipulate Immune Receptor Signaling and Immune Cell Fates. Adv Healthc Mater 2022; 11:e2101844. [PMID: 34716686 DOI: 10.1002/adhm.202101844] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/14/2021] [Indexed: 12/19/2022]
Abstract
Immune cells sense, communicate, and logically integrate a multitude of environmental signals to make important cell-fate decisions and fulfill their effector functions. These processes are initiated and regulated by a diverse array of immune receptors and via their dynamic spatiotemporal organization upon ligand binding. Given the widespread relevance of the immune system to health and disease, there have been significant efforts toward understanding the biophysical principles governing immune receptor signaling and activation, as well as the development of biomaterials which exploit these principles for therapeutic immune engineering. Here, how advances in the field of DNA nanotechnology constitute a growing toolbox for further pursuit of these endeavors is discussed. Key cellular players involved in the induction of immunity against pathogens or diseased cells are first summarized. How the ability to design DNA nanostructures with custom shapes, dynamics, and with site-specific incorporation of diverse guests can be leveraged to manipulate the signaling pathways that regulate these processes is then presented. It is followed by highlighting emerging applications of DNA nanotechnology at the crossroads of immune engineering, such as in vitro reconstitution platforms, vaccines, and adjuvant delivery systems. Finally, outstanding questions that remain for further advancing immune-modulatory DNA nanodevices are outlined.
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Affiliation(s)
- Chung Yi Tseng
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
| | - Wendy Xueyi Wang
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
| | - Travis Robert Douglas
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
| | - Leo Y. T. Chou
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
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107
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Freitas AI, Domingues L, Aguiar TQ. Tag-mediated single-step purification and immobilization of recombinant proteins toward protein-engineered advanced materials. J Adv Res 2022; 36:249-264. [PMID: 35127175 PMCID: PMC8799874 DOI: 10.1016/j.jare.2021.06.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 06/08/2021] [Accepted: 06/10/2021] [Indexed: 12/12/2022] Open
Abstract
Background The potential applications of protein-engineered functional materials are so wide and exciting that the interest in these eco-friendly advanced materials will further expand in the future. Tag-mediated protein purification/immobilization technologies have emerged as green and cost-effective approaches for the fabrication of such materials. Strategies that combine the purification and immobilization of recombinant proteins/peptides onto/into natural, synthetic or hybrid materials in a single-step are arising and attracting increasing interest. Aim of Review This review highlights the most significant advances of the last 5 years within the scope of tag-mediated protein purification/immobilization and elucidates their contributions for the development of efficient single-step purification and immobilization strategies. Recent progresses in the field of protein-engineered materials created using innovative protein-tag combinations and future opportunities created by these new technologies are also summarized and identified herein. Key Scientific Concepts of Review Protein purification/immobilization tags present a remarkable ability to establish specific non-covalent/covalent interactions between solid materials and biological elements, which prompted the creation of tailor-made and advanced functional materials, and of next-generation hybrid materials. Affinity tags can bind to a wide range of materials (of synthetic, natural or hybrid nature), being most suitable for protein purification. Covalently binding tags are most suitable for long-term protein immobilization, but can only bind naturally to protein-based materials. Hybrid affinity-covalently binding tags have allowed efficient one-step purification and immobilization of proteins onto different materials, as well as the development of innovative protein-engineered materials. Self-aggregating tags have been particularly useful in combination with other tags for generating protein-engineered materials with self-assembling, flexible and/or responsive properties. While these tags have been mainly explored for independent protein purification, immobilization or functionalization purposes, efficient strategies that combine tag-mediated purification and immobilization/functionalization in a single-step will be essential to guarantee the sustainable manufacturing of advanced protein-engineered materials.
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Affiliation(s)
- Ana I. Freitas
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Tatiana Q. Aguiar
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
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108
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Wei J, Xu L, Wu WH, Sun F, Zhang WB. Genetically engineered materials: Proteins and beyond. Sci China Chem 2022; 65:486-496. [PMID: 35154293 PMCID: PMC8815391 DOI: 10.1007/s11426-021-1183-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/21/2021] [Indexed: 02/01/2023]
Abstract
Information-rich molecules provide opportunities for evolution. Genetically engineered materials are superior in that their properties are coded within genetic sequences and could be fine-tuned. In this review, we elaborate the concept of genetically engineered materials (GEMs) using examples ranging from engineered protein materials to engineered living materials. Protein-based materials are the materials of choice by nature. Recent progress in protein engineering has led to opportunities to tune their sequences for optimal material performance. Proteins also play a central role in living materials where they act in concert with other biological components as well as nonbiological cofactors, giving rise to living features. While the existing GEMs are often limited to those constructed by building blocks of biological origin, being genetically engineerable does not preclude nonbiologic or synthetic materials, the latter of which have yet to be fully explored.
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Affiliation(s)
- Jingjing Wei
- College of Chemical and Environmental Engineering, Anyang Institute of Technology, Anyang, 455000 China
| | - Lianjie Xu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871 China
| | - Wen-Hao Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871 China
| | - Fei Sun
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871 China
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109
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Fok HKF, Yang Z, Jiang B, Sun F. From 4-arm star proteins to diverse stimuli-responsive molecular networks enabled by orthogonal genetically encoded click chemistries. Polym Chem 2022. [DOI: 10.1039/d2py00036a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The integrated use of genetically encoded click chemistries and protein topology engineering enabled the creation of various smart protein hydrogels.
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Affiliation(s)
- Hong Kiu Francis Fok
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Zhongguang Yang
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Bojing Jiang
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Fei Sun
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518036, China
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110
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Pedroso CC, Mann VR, Zuberbühler K, Bohn MF, Yu J, Altoe V, Craik CS, Cohen BE. Immunotargeting of Nanocrystals by SpyCatcher Conjugation of Engineered Antibodies. ACS NANO 2021; 15:18374-18384. [PMID: 34694776 PMCID: PMC9035480 DOI: 10.1021/acsnano.1c07856] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Inorganic nanocrystals such as quantum dots (QDs) and upconverting nanoparticles (UCNPs) are uniquely suited for quantitative live-cell imaging and are typically functionalized with ligands to study specific receptors or cellular targets. Antibodies (Ab) are among the most useful targeting reagents owing to their high affinities and specificities, but common nanocrystal labeling methods may orient Ab incorrectly, be reversible or denaturing, or lead to Ab-NP complexes too large for some applications. Here, we show that SpyCatcher proteins, which bind and spontaneously form covalent isopeptide bonds with cognate SpyTag peptides, can conjugate engineered Ab to nanoparticle surfaces with control over stability, orientation, and stoichiometry. Compact SpyCatcher-functionalized QDs and UCNPs may be labeled with short-chain variable fragment Ab (scFv) engineered to bind urokinase-type plasminogen activator receptors (uPAR) that are overexpressed in many human cancers. Confocal imaging of anti-uPAR scFv-QD conjugates shows the antibody mediates specific binding and internalization by breast cancer cells expressing uPAR. Time-lapse imaging of photostable scFv-UCNP conjugates shows that Ab binding causes uPAR internalization with a ∼20 min half-life on the cell surface, and uPAR is internalized to endolysosomal compartments distinct from general membrane stains and without significant recycling to the cell surface. The controlled and stable conjugation of engineered Ab to NPs enables targeting of diverse receptors for live-cell study of their distribution, trafficking, and physiology.
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Affiliation(s)
- Cassio C.S. Pedroso
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Victor R. Mann
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Kathrin Zuberbühler
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94143, United States
| | - Markus-Frederik Bohn
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94143, United States
| | - Jessica Yu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Virginia Altoe
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Charles S. Craik
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94143, United States
| | - Bruce E. Cohen
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Division of Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Corresponding Author:
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111
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Herdman M, von Kügelgen A, Kureisaite-Ciziene D, Duman R, El Omari K, Garman EF, Kjaer A, Kolokouris D, Löwe J, Wagner A, Stansfeld PJ, Bharat TAM. High-resolution mapping of metal ions reveals principles of surface layer assembly in Caulobacter crescentus cells. Structure 2021; 30:215-228.e5. [PMID: 34800371 PMCID: PMC8828063 DOI: 10.1016/j.str.2021.10.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 08/17/2021] [Accepted: 10/22/2021] [Indexed: 12/02/2022]
Abstract
Surface layers (S-layers) are proteinaceous crystalline coats that constitute the outermost component of most prokaryotic cell envelopes. In this study, we have investigated the role of metal ions in the formation of the Caulobacter crescentus S-layer using high-resolution structural and cell biology techniques, as well as molecular simulations. Utilizing optical microscopy of fluorescently tagged S-layers, we show that calcium ions facilitate S-layer lattice formation and cell-surface binding. We report all-atom molecular dynamics simulations of the S-layer lattice, revealing the importance of bound metal ions. Finally, using electron cryomicroscopy and long-wavelength X-ray diffraction experiments, we mapped the positions of metal ions in the S-layer at near-atomic resolution, supporting our insights from the cellular and simulations data. Our findings contribute to the understanding of how C. crescentus cells form a regularly arranged S-layer on their surface, with implications on fundamental S-layer biology and the synthetic biology of self-assembling biomaterials. Live imaging shows Ca2+-dependent expansion of the C. crescentus S-layer Molecular simulations reveal Ca2+-binding properties of the S-layer Ca2+ ion mapping in three-dimensional crystals using in-vacuum X-ray anomalous diffraction Ca2+ replacement by Ho3+ allows cryo-EM mapping of heavy metals
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Affiliation(s)
- Matthew Herdman
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | | | | | - Ramona Duman
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Kamel El Omari
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Andreas Kjaer
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | | | - Jan Löwe
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Armin Wagner
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Phillip J Stansfeld
- School of Life Sciences and Department of Chemistry, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL, UK.
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
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112
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Collins LT, Curiel DT. Synthetic Biology Approaches for Engineering Next-Generation Adenoviral Gene Therapies. ACS NANO 2021; 15:13970-13979. [PMID: 34415739 DOI: 10.1021/acsnano.1c04556] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Synthetic biology centers on the design and modular assembly of biological parts so as to construct artificial biological systems. Over the past decade, synthetic biology has blossomed into a highly productive field, yielding advances in diverse areas such as neuroscience, cell-based therapies, and chemical manufacturing. Similarly, the field of gene therapy has made enormous strides both in proof-of-concept studies and in the clinical setting. One viral vector of increasing interest for gene therapy is the adenovirus (Ad). A major part of the Ad's increasing momentum comes from synthetic biology approaches to Ad engineering. Convergence of gene therapy and synthetic biology has enhanced Ad vectors by mitigating Ad toxicity in vivo, providing precise Ad tropisms, and incorporating genetic circuits to make smart therapies which adapt to environmental stimuli. Synthetic biology engineering of Ad vectors may lead to superior gene delivery and editing platforms which could find applications in a wide range of therapeutic contexts.
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Affiliation(s)
- Logan Thrasher Collins
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri 63110, United States
| | - David T Curiel
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri 63110, United States
- Department of Radiation Oncology, Washington University in St. Louis, St. Louis, Missouri 63110, United States
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113
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Zhu J, Ananthaswamy N, Jain S, Batra H, Tang WC, Lewry DA, Richards ML, David SA, Kilgore PB, Sha J, Drelich A, Tseng CTK, Chopra AK, Rao VB. A universal bacteriophage T4 nanoparticle platform to design multiplex SARS-CoV-2 vaccine candidates by CRISPR engineering. SCIENCE ADVANCES 2021; 7:eabh1547. [PMID: 34516878 PMCID: PMC8442874 DOI: 10.1126/sciadv.abh1547] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/16/2021] [Indexed: 06/02/2023]
Abstract
A “universal” platform that can rapidly generate multiplex vaccine candidates is critically needed to control pandemics. Using the severe acute respiratory syndrome coronavirus 2 as a model, we have developed such a platform by CRISPR engineering of bacteriophage T4. A pipeline of vaccine candidates was engineered by incorporating various viral components into appropriate compartments of phage nanoparticle structure. These include expressible spike genes in genome, spike and envelope epitopes as surface decorations, and nucleocapsid proteins in packaged core. Phage decorated with spike trimers was found to be the most potent vaccine candidate in animal models. Without any adjuvant, this vaccine stimulated robust immune responses, both T helper cell 1 (TH1) and TH2 immunoglobulin G subclasses, blocked virus-receptor interactions, neutralized viral infection, and conferred complete protection against viral challenge. This new nanovaccine design framework might allow the rapid deployment of effective adjuvant-free phage-based vaccines against any emerging pathogen in the future.
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Affiliation(s)
- Jingen Zhu
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC 20064, USA
| | - Neeti Ananthaswamy
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC 20064, USA
| | - Swati Jain
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC 20064, USA
| | - Himanshu Batra
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC 20064, USA
| | - Wei-Chun Tang
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC 20064, USA
| | | | | | | | - Paul B. Kilgore
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jian Sha
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Aleksandra Drelich
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Chien-Te K. Tseng
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Ashok K. Chopra
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Venigalla B. Rao
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC 20064, USA
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114
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Chauhan K, Zárate‐Romero A, Sengar P, Medrano C, Vazquez‐Duhalt R. Catalytic Kinetics Considerations and Molecular Tools for the Design of Multienzymatic Cascade Nanoreactors. ChemCatChem 2021. [DOI: 10.1002/cctc.202100604] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Kanchan Chauhan
- Department of Bionanotechnology Center for Nanosciences and Nanotechnology Universidad Nacional Autónoma de México Km 107 carretera Tijuana-Ensenada Ensenada Baja California 22860 Mexico
| | - Andrés Zárate‐Romero
- Department of Bionanotechnology Center for Nanosciences and Nanotechnology Universidad Nacional Autónoma de México Km 107 carretera Tijuana-Ensenada Ensenada Baja California 22860 Mexico
- Cátedra Consejo Nacional de Ciencia y Tecnología CNyN-UNAM Ensenada Baja California 22860 Mexico
| | - Prakhar Sengar
- Department of Bionanotechnology Center for Nanosciences and Nanotechnology Universidad Nacional Autónoma de México Km 107 carretera Tijuana-Ensenada Ensenada Baja California 22860 Mexico
| | - Carlos Medrano
- Department of Bionanotechnology Center for Nanosciences and Nanotechnology Universidad Nacional Autónoma de México Km 107 carretera Tijuana-Ensenada Ensenada Baja California 22860 Mexico
| | - Rafael Vazquez‐Duhalt
- Department of Bionanotechnology Center for Nanosciences and Nanotechnology Universidad Nacional Autónoma de México Km 107 carretera Tijuana-Ensenada Ensenada Baja California 22860 Mexico
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115
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Lei H, Ma Q, Li W, Wen J, Ma H, Qin M, Wang W, Cao Y. An ester bond underlies the mechanical strength of a pathogen surface protein. Nat Commun 2021; 12:5082. [PMID: 34426584 PMCID: PMC8382745 DOI: 10.1038/s41467-021-25425-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 08/10/2021] [Indexed: 11/23/2022] Open
Abstract
Gram-positive bacteria can resist large mechanical perturbations during their invasion and colonization by secreting various surface proteins with intramolecular isopeptide or ester bonds. Compared to isopeptide bonds, ester bonds are prone to hydrolysis. It remains elusive whether ester bonds can completely block mechanical extension similarly to isopeptide bonds, or whether ester bonds dissipate mechanical energy by bond rupture. Here, we show that an ester-bond containing stalk domain of Cpe0147 is inextensible even at forces > 2 nN. The ester bond locks the structure to a partially unfolded conformation, in which the ester bond remains largely water inaccessible. This allows the ester bond to withstand considerable mechanical forces and in turn prevent complete protein unfolding. However, the protecting effect might be reduced at non-physiological basic pHs or low calcium concentrations due to destabilizing the protein structures. Inspired by this design principle, we engineer a disulfide mutant resistant to mechanical unfolding under reducing conditions. Bacterial surface adhesion proteins are characterized by unusual mechanical properties. Here, the authors use atomic force microscopy-based technique to study a surface-anchoring protein Cpe0147 from Clostridium perfringens and show that an ester bond can withstand considerable mechanical forces and prevent complete protein unfolding.
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Affiliation(s)
- Hai Lei
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, China.,Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China
| | - Quan Ma
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, China
| | - Wenfei Li
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, China
| | - Jing Wen
- Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing, China
| | - Haibo Ma
- Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing, China
| | - Meng Qin
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, China
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, China. .,Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China.
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116
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Keeble AH, Yadav VK, Ferla MP, Bauer CC, Chuntharpursat-Bon E, Huang J, Bon RS, Howarth M. DogCatcher allows loop-friendly protein-protein ligation. Cell Chem Biol 2021; 29:339-350.e10. [PMID: 34324879 PMCID: PMC8878318 DOI: 10.1016/j.chembiol.2021.07.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/09/2021] [Accepted: 07/02/2021] [Indexed: 12/14/2022]
Abstract
There are many efficient ways to connect proteins at termini. However, connecting at a loop is difficult because of lower flexibility and variable environment. Here, we have developed DogCatcher, a protein that forms a spontaneous isopeptide bond with DogTag peptide. DogTag/DogCatcher was generated initially by splitting a Streptococcus pneumoniae adhesin. We optimized DogTag/DogCatcher through rational design and evolution, increasing reaction rate by 250-fold and establishing millimolar solubility of DogCatcher. When fused to a protein terminus, DogTag/DogCatcher reacts slower than SpyTag003/SpyCatcher003. However, inserted in loops of a fluorescent protein or enzyme, DogTag reacts much faster than SpyTag003. Like many membrane proteins, the ion channel TRPC5 has no surface-exposed termini. DogTag in a TRPC5 extracellular loop allowed normal calcium flux and specific covalent labeling on cells in 1 min. DogTag/DogCatcher reacts under diverse conditions, at nanomolar concentrations, and to 98% conversion. Loop-friendly ligation should expand the toolbox for creating protein architectures. Spontaneous transamidation at internal sites harnessing a DogTag/DogCatcher pair DogCatcher is designed and bred for high solubility and rapid reaction Within protein loops DogTag can clamp on its partner faster than SpyTag003 Fast and faithful fluorescent labeling of an ion channel at the cell surface via DogTag
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Affiliation(s)
- Anthony H Keeble
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Vikash K Yadav
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Matteo P Ferla
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Claudia C Bauer
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Eulashini Chuntharpursat-Bon
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Jin Huang
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Robin S Bon
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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117
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Da XD, Wu XL, Liu Y, Zhang WB. Protein Conjugation via SpyStapler-Mediated SpyTag/BDTag Coupling. Curr Protoc 2021; 1:e99. [PMID: 33826806 DOI: 10.1002/cpz1.99] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Genetically encoded peptide-protein coupling reactions, such as the SpyTag/SpyCatcher chemistry, are recent additions to the expanding toolbox of protein bioconjugation. The alternative three-component ligation system, e.g., SpyStapler-mediated SpyTag/BDTag coupling, retains most advantages of the Tag/Catcher chemistry, yet requires only two short peptide tags in the genetic fusion for side-chain ligation. Not only does this facilitate the construction of large protein conjugates directly from as-expressed protein components with minimal disruption to their function, but it also provides an entirely new mode of bioconjugation via mechanical bonding, which could impart additional functional benefits such as improved activity and enhanced stability to the conjugate. Such features are attractive for improving the pharmacokinetic performance of protein therapeutics. Herein we describe protocols for SpyStapler-mediated SpyTag/BDTag coupling for protein bioconjugation. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Conjugation via isopeptide bond Support Protocol: Purification by size-exclusion chromatography Basic Protocol 2: Conjugation via mechanical bond.
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Affiliation(s)
- Xiao-Di Da
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Xia-Ling Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Yajie Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
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118
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Hartzell EJ, Terr J, Chen W. Engineering a Blue Light Inducible SpyTag System (BLISS). J Am Chem Soc 2021; 143:8572-8577. [PMID: 34077186 DOI: 10.1021/jacs.1c03198] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The SpyCatcher/SpyTag protein conjugation system has recently exploded in popularity due to its fast kinetics and high yield under biologically favorable conditions in both in vitro and intracellular settings. The utility of this system could be expanded by introducing the ability to spatially and temporally control the conjugation event. Taking inspiration from photoreceptor proteins in nature, we designed a method to integrate light dependency into the protein conjugation reaction. The light-oxygen-voltage domain 2 of Avena sativa (AsLOV2) undergoes a dramatic conformational change in its c-terminal Jα-helix in response to blue light. By inserting SpyTag into the different locations of the Jα-helix, we created a blue light inducible SpyTag system (BLISS). In this design, the SpyTag is blocked from reacting with the SpyCatcher in the dark, but upon irradiation with blue light, the Jα-helix of the AsLOV2 undocks to expose the SpyTag. We tested several insertion sites and characterized the kinetics. We found three variants with dynamic ranges over 15, which were active within different concentration ranges. These could be tuned using SpyCatcher variants with different reaction kinetics. Further, the reaction could be instantaneously quenched by removing light. We demonstrated the spatial aspect of this light control mechanism through photopatterning of two fluorescent proteins. This system offers opportunities for many other biofabrication and optogenetics applications.
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Affiliation(s)
- Emily J Hartzell
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Justin Terr
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
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119
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Aebischer A, Wernike K, König P, Franzke K, Wichgers Schreur PJ, Kortekaas J, Vitikainen M, Wiebe M, Saloheimo M, Tchelet R, Audonnet JC, Beer M. Development of a Modular Vaccine Platform for Multimeric Antigen Display Using an Orthobunyavirus Model. Vaccines (Basel) 2021; 9:vaccines9060651. [PMID: 34203630 PMCID: PMC8232151 DOI: 10.3390/vaccines9060651] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/04/2021] [Accepted: 06/08/2021] [Indexed: 12/15/2022] Open
Abstract
Emerging infectious diseases represent an increasing threat to human and animal health. Therefore, safe and effective vaccines that could be available within a short time frame after an outbreak are required for adequate prevention and control. Here, we developed a robust and versatile self-assembling multimeric protein scaffold particle (MPSP) vaccine platform using lumazine synthase (LS) from Aquifex aeolicus. This scaffold allowed the presentation of peptide epitopes by genetic fusion as well as the presentation of large antigens by bacterial superglue-based conjugation to the pre-assembled particle. Using the orthobunyavirus model Schmallenberg virus (SBV) we designed MPSPs presenting major immunogens of SBV and assessed their efficacy in a mouse model as well as in cattle, a target species of SBV. All prototype vaccines conferred protection from viral challenge infection and the multivalent presentation of the selected antigens on the MPSP markedly improved their immunogenicity compared to the monomeric subunits. Even a single shot vaccination protected about 80% of mice from an otherwise lethal dose of SBV. Most importantly, the MPSPs induced a virtually sterile immunity in cattle. Altogether, LS represents a promising platform for modular and rapid vaccine design.
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Affiliation(s)
- Andrea Aebischer
- Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (A.A.); (K.W.); (P.K.); (K.F.)
| | - Kerstin Wernike
- Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (A.A.); (K.W.); (P.K.); (K.F.)
| | - Patricia König
- Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (A.A.); (K.W.); (P.K.); (K.F.)
| | - Kati Franzke
- Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (A.A.); (K.W.); (P.K.); (K.F.)
| | - Paul J. Wichgers Schreur
- Laboratory of Virology, Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands; (P.J.W.S.); (J.K.)
| | - Jeroen Kortekaas
- Laboratory of Virology, Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands; (P.J.W.S.); (J.K.)
| | - Marika Vitikainen
- VTT Technical Research Centre of Finland Ltd., 02150 Espoo, Finland; (M.V.); (M.W.); (M.S.)
| | - Marilyn Wiebe
- VTT Technical Research Centre of Finland Ltd., 02150 Espoo, Finland; (M.V.); (M.W.); (M.S.)
| | - Markku Saloheimo
- VTT Technical Research Centre of Finland Ltd., 02150 Espoo, Finland; (M.V.); (M.W.); (M.S.)
| | - Ronen Tchelet
- Dyadic Netherland B.V., 6709 PA Wageningen, The Netherlands;
| | | | - Martin Beer
- Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (A.A.); (K.W.); (P.K.); (K.F.)
- Correspondence:
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120
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Hörner M, Jerez-Longres C, Hudek A, Hook S, Yousefi OS, Schamel WWA, Hörner C, Zurbriggen MD, Ye H, Wagner HJ, Weber W. Spatiotemporally confined red light-controlled gene delivery at single-cell resolution using adeno-associated viral vectors. SCIENCE ADVANCES 2021; 7:7/25/eabf0797. [PMID: 34134986 PMCID: PMC8208708 DOI: 10.1126/sciadv.abf0797] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 05/04/2021] [Indexed: 05/15/2023]
Abstract
Methodologies for the controlled delivery of genetic information into target cells are of utmost importance for genetic engineering in both fundamental and applied research. However, available methods for efficient gene transfer into user-selected or even single cells suffer from low throughput, the need for complicated equipment, high invasiveness, or side effects by off-target viral uptake. Here, we engineer an adeno-associated viral (AAV) vector system that transfers genetic information into native target cells upon illumination with cell-compatible red light. This OptoAAV system allows adjustable and spatially resolved gene transfer down to single-cell resolution and is compatible with different cell lines and primary cells. Moreover, the sequential application of multiple OptoAAVs enables spatially resolved transduction with different transgenes. The approach presented is likely extendable to other classes of viral vectors and is expected to foster advances in basic and applied genetic research.
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Affiliation(s)
- Maximilian Hörner
- Faculty of Biology, University of Freiburg, Freiburg, Germany.
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Carolina Jerez-Longres
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Anna Hudek
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Sebastian Hook
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - O Sascha Yousefi
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Center of Chronic Immunodeficiency CCI, University Clinics and Medical Faculty, Freiburg, Germany
| | - Wolfgang W A Schamel
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Center of Chronic Immunodeficiency CCI, University Clinics and Medical Faculty, Freiburg, Germany
| | - Cindy Hörner
- Division of Veterinary Medicine, Paul-Ehrlich-Institut, Langen, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Haifeng Ye
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Hanna J Wagner
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Wilfried Weber
- Faculty of Biology, University of Freiburg, Freiburg, Germany.
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
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121
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Kajiwara K, Aoki W, Koike N, Ueda M. Development of a yeast cell surface display method using the SpyTag/SpyCatcher system. Sci Rep 2021; 11:11059. [PMID: 34040114 PMCID: PMC8155107 DOI: 10.1038/s41598-021-90593-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/12/2021] [Indexed: 12/05/2022] Open
Abstract
Yeast cell surface display (YSD) has been used to engineer various proteins, including antibodies. Directed evolution, which subjects a gene to iterative rounds of mutagenesis, selection and amplification, is useful for protein engineering. In vivo continuous mutagenesis, which continuously diversifies target genes in the host cell, is a promising tool for accelerating directed evolution. However, combining in vivo continuous evolution and YSD is difficult because mutations in the gene encoding the anchor proteins may inhibit the display of target proteins on the cell surface. In this study, we have developed a modified YSD method that utilises SpyTag/SpyCatcher-based in vivo protein ligation. A nanobody fused with a SpyTag of 16 amino acids and an anchor protein fused with a SpyCatcher of 113 amino acids are encoded by separate gene cassettes and then assembled via isopeptide bond formation. This system achieved a high display efficiency of more than 90%, no intercellular protein ligation events, and the enrichment of target cells by cell sorting. These results suggested that our system demonstrates comparable performance with conventional YSD methods; therefore, it can be an appropriate platform to be integrated with in vivo continuous evolution.
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Affiliation(s)
- Kaho Kajiwara
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
- JST, CREST, 7 Goban-cho, Chiyoda-ku, Tokyo, 102-0076, Japan
| | - Naoki Koike
- TechnoPro, Inc. TechnoPro R&D, Company, Tokyo, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan.
- JST, CREST, 7 Goban-cho, Chiyoda-ku, Tokyo, 102-0076, Japan.
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122
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Fredsgaard L, Goksøyr L, Thrane S, Aves KL, Theander TG, Sander AF. Head-to-Head Comparison of Modular Vaccines Developed Using Different Capsid Virus-Like Particle Backbones and Antigen Conjugation Systems. Vaccines (Basel) 2021; 9:vaccines9060539. [PMID: 34063871 PMCID: PMC8224050 DOI: 10.3390/vaccines9060539] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 01/19/2023] Open
Abstract
Capsid virus-like particles (cVLPs) are used as molecular scaffolds to increase the immunogenicity of displayed antigens. Modular platforms have been developed whereby antigens are attached to the surface of pre-assembled cVLPs. However, it remains unknown to what extent the employed cVLP backbone and conjugation system may influence the immune response elicited against the displayed antigen. Here, we performed a head-to-head comparison of antigen-specific IgG responses elicited by modular cVLP-vaccines differing by their employed cVLP backbone or conjugation system, respectively. Covalent antigen conjugation (i.e., employing the SpyTag/SpyCatcher system) resulted in significantly higher antigen-specific IgG titers compared to when using affinity-based conjugation (i.e., using biotin/streptavidin). The cVLP backbone also influenced the antigen-specific IgG response. Specifically, vaccines based on the bacteriophage AP205 cVLP elicited significantly higher antigen-specific IgG compared to corresponding vaccines using the human papillomavirus major capsid protein (HPV L1) cVLP. In addition, the AP205 cVLP platform mediated induction of antigen-specific IgG with a different subclass profile (i.e., higher IgG2a and IgG2b) compared to HPV L1 cVLP. These results demonstrate that the cVLP backbone and conjugation system can individually affect the IgG response elicited against a displayed antigen. These data will aid the understanding and process of tailoring modular cVLP vaccines to achieve improved immune responses.
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Affiliation(s)
- Laurits Fredsgaard
- Centre for Medical Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (L.F.); (L.G.); (K.-L.A.); (T.G.T.)
| | - Louise Goksøyr
- Centre for Medical Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (L.F.); (L.G.); (K.-L.A.); (T.G.T.)
- AdaptVac Aps, 2970 Hørsholm, Denmark;
| | | | - Kara-Lee Aves
- Centre for Medical Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (L.F.); (L.G.); (K.-L.A.); (T.G.T.)
| | - Thor G. Theander
- Centre for Medical Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (L.F.); (L.G.); (K.-L.A.); (T.G.T.)
| | - Adam F. Sander
- Centre for Medical Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (L.F.); (L.G.); (K.-L.A.); (T.G.T.)
- AdaptVac Aps, 2970 Hørsholm, Denmark;
- Correspondence:
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Structural and functional analysis of LIM domain-dependent recruitment of paxillin to αvβ3 integrin-positive focal adhesions. Commun Biol 2021; 4:380. [PMID: 33782527 PMCID: PMC8007706 DOI: 10.1038/s42003-021-01886-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 02/11/2021] [Indexed: 02/06/2023] Open
Abstract
The LIM domain-dependent localization of the adapter protein paxillin to β3 integrin-positive focal adhesions (FAs) is not mechanistically understood. Here, by combining molecular biology, photoactivation and FA-isolation experiments, we demonstrate specific contributions of each LIM domain of paxillin and reveal multiple paxillin interactions in adhesion-complexes. Mutation of β3 integrin at a putative paxillin binding site (β3VE/YA) leads to rapidly inward-sliding FAs, correlating with actin retrograde flow and enhanced paxillin dissociation kinetics. Induced mechanical coupling of paxillin to β3VE/YA integrin arrests the FA-sliding, thereby disclosing an essential structural function of paxillin for the maturation of β3 integrin/talin clusters. Moreover, bimolecular fluorescence complementation unveils the spatial orientation of the paxillin LIM-array, juxtaposing the positive LIM4 to the plasma membrane and the β3 integrin-tail, while in vitro binding assays point to LIM1 and/or LIM2 interaction with talin-head domain. These data provide structural insights into the molecular organization of β3 integrin-FAs.
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124
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Mann VR, Manea F, Borys NJ, Ajo-Franklin CM, Cohen BE. Controlled and Stable Patterning of Diverse Inorganic Nanocrystals on Crystalline Two-Dimensional Protein Arrays. Biochemistry 2021; 60:1063-1074. [PMID: 33691067 DOI: 10.1021/acs.biochem.1c00032] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Controlled patterning of nanoparticles on bioassemblies enables synthesis of complex materials for applications in optics, nanoelectronics, and sensing. Biomolecular self-assembly offers molecular control for engineering patterned nanomaterials, but current approaches have been limited in their ability to combine high nanoparticle coverage with generality that enables incorporation of multiple nanoparticle types. Here, we synthesize photonic materials on crystalline two-dimensional (2D) protein sheets using orthogonal bioconjugation reactions, organizing quantum dots (QDs), gold nanoparticles (AuNPs), and upconverting nanoparticles along the surface-layer (S-layer) protein SbsB from the extremophile Geobacillus stearothermophilus. We use electron and optical microscopy to show that isopeptide bond-forming SpyCatcher and SnoopCatcher systems enable the simultaneous and controlled conjugation of multiple types of nanoparticles (NPs) at high densities along the SbsB sheets. These NP conjugation reactions are orthogonal to each other and to Au-thiol bond formation, allowing tailorable nanoparticle combinations at sufficient labeling efficiencies to permit optical interactions between nanoparticles. Fluorescence lifetime imaging of SbsB sheets conjugated to QDs and AuNPs at distinct attachment sites shows spatially heterogeneous QD emission, with shorter radiative decays and brighter fluorescence arising from plasmonic enhancement at short interparticle distances. This specific, stable, and efficient conjugation of NPs to 2D protein sheets enables the exploration of interactions between pairs of nanoparticles at defined distances for the engineering of protein-based photonic nanomaterials.
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125
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Kang YF, Sun C, Zhuang Z, Yuan RY, Zheng Q, Li JP, Zhou PP, Chen XC, Liu Z, Zhang X, Yu XH, Kong XW, Zhu QY, Zhong Q, Xu M, Zhong NS, Zeng YX, Feng GK, Ke C, Zhao JC, Zeng MS. Rapid Development of SARS-CoV-2 Spike Protein Receptor-Binding Domain Self-Assembled Nanoparticle Vaccine Candidates. ACS NANO 2021; 15:2738-2752. [PMID: 33464829 PMCID: PMC7839421 DOI: 10.1021/acsnano.0c08379] [Citation(s) in RCA: 137] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/13/2021] [Indexed: 05/18/2023]
Abstract
The coronavirus disease pandemic of 2019 (COVID-19) caused by the novel SARS-CoV-2 coronavirus resulted in economic losses and threatened human health worldwide. The pandemic highlights an urgent need for a stable, easily produced, and effective vaccine. SARS-CoV-2 uses the spike protein receptor-binding domain (RBD) to bind its cognate receptor, angiotensin-converting enzyme 2 (ACE2), and initiate membrane fusion. Thus, the RBD is an ideal target for vaccine development. In this study, we designed three different RBD-conjugated nanoparticle vaccine candidates, namely, RBD-Ferritin (24-mer), RBD-mi3 (60-mer), and RBD-I53-50 (120-mer), via covalent conjugation using the SpyTag-SpyCatcher system. When mice were immunized with the RBD-conjugated nanoparticles (NPs) in conjunction with the AddaVax or Sigma Adjuvant System, the resulting antisera exhibited 8- to 120-fold greater neutralizing activity against both a pseudovirus and the authentic virus than those of mice immunized with monomeric RBD. Most importantly, sera from mice immunized with RBD-conjugated NPs more efficiently blocked the binding of RBD to ACE2 in vitro, further corroborating the promising immunization effect. Additionally, the vaccine has distinct advantages in terms of a relatively simple scale-up and flexible assembly. These results illustrate that the SARS-CoV-2 RBD-conjugated nanoparticles developed in this study are a competitive vaccine candidate and that the carrier nanoparticles could be adopted as a universal platform for a future vaccine development.
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Affiliation(s)
- Yin-Feng Kang
- State Key Laboratory of Oncology in South China,
Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of
Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research,
Sun Yat-sen University Cancer Center, Sun Yat-sen University,
Guangzhou 510060, P. R. China
| | - Cong Sun
- State Key Laboratory of Oncology in South China,
Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of
Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research,
Sun Yat-sen University Cancer Center, Sun Yat-sen University,
Guangzhou 510060, P. R. China
| | - Zhen Zhuang
- State Key Laboratory of Respiratory Disease, National
Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory
Health, The First Affiliated Hospital of Guangzhou Medical
University, Guangzhou 510182, P. R. China
| | - Run-Yu Yuan
- Guangdong Provincial Institution of Public Health,
Guangdong Provincial Center for Disease Control and
Prevention, Guangzhou 511430, P. R. China
| | - Qingbing Zheng
- State Key Laboratory of Molecular Vaccinology and
Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in
Infectious Diseases, School of Public Health, Xiamen
University, Xiamen 361102, P. R. China
| | - Jiang-Ping Li
- State Key Laboratory of Oncology in South China,
Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of
Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research,
Sun Yat-sen University Cancer Center, Sun Yat-sen University,
Guangzhou 510060, P. R. China
| | - Ping-Ping Zhou
- Guangdong Provincial Institution of Public Health,
Guangdong Provincial Center for Disease Control and
Prevention, Guangzhou 511430, P. R. China
| | - Xin-Chun Chen
- State Key Laboratory of Oncology in South China,
Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of
Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research,
Sun Yat-sen University Cancer Center, Sun Yat-sen University,
Guangzhou 510060, P. R. China
| | - Zhe Liu
- Guangdong Provincial Institution of Public Health,
Guangdong Provincial Center for Disease Control and
Prevention, Guangzhou 511430, P. R. China
| | - Xiao Zhang
- State Key Laboratory of Oncology in South China,
Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of
Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research,
Sun Yat-sen University Cancer Center, Sun Yat-sen University,
Guangzhou 510060, P. R. China
| | - Xiao-Hui Yu
- State Key Laboratory of Oncology in South China,
Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of
Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research,
Sun Yat-sen University Cancer Center, Sun Yat-sen University,
Guangzhou 510060, P. R. China
| | - Xiang-Wei Kong
- State Key Laboratory of Oncology in South China,
Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of
Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research,
Sun Yat-sen University Cancer Center, Sun Yat-sen University,
Guangzhou 510060, P. R. China
| | - Qian-Ying Zhu
- State Key Laboratory of Oncology in South China,
Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of
Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research,
Sun Yat-sen University Cancer Center, Sun Yat-sen University,
Guangzhou 510060, P. R. China
| | - Qian Zhong
- State Key Laboratory of Oncology in South China,
Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of
Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research,
Sun Yat-sen University Cancer Center, Sun Yat-sen University,
Guangzhou 510060, P. R. China
| | - Miao Xu
- State Key Laboratory of Oncology in South China,
Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of
Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research,
Sun Yat-sen University Cancer Center, Sun Yat-sen University,
Guangzhou 510060, P. R. China
| | - Nan-Shan Zhong
- State Key Laboratory of Respiratory Disease, National
Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory
Health, The First Affiliated Hospital of Guangzhou Medical
University, Guangzhou 510182, P. R. China
| | - Yi-Xin Zeng
- State Key Laboratory of Oncology in South China,
Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of
Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research,
Sun Yat-sen University Cancer Center, Sun Yat-sen University,
Guangzhou 510060, P. R. China
| | - Guo-Kai Feng
- State Key Laboratory of Oncology in South China,
Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of
Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research,
Sun Yat-sen University Cancer Center, Sun Yat-sen University,
Guangzhou 510060, P. R. China
| | - Changwen Ke
- Guangdong Provincial Institution of Public Health,
Guangdong Provincial Center for Disease Control and
Prevention, Guangzhou 511430, P. R. China
| | - Jin-Cun Zhao
- State Key Laboratory of Respiratory Disease, National
Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory
Health, The First Affiliated Hospital of Guangzhou Medical
University, Guangzhou 510182, P. R. China
| | - Mu-Sheng Zeng
- State Key Laboratory of Oncology in South China,
Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of
Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research,
Sun Yat-sen University Cancer Center, Sun Yat-sen University,
Guangzhou 510060, P. R. China
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126
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Cohen AA, Gnanapragasam PNP, Lee YE, Hoffman PR, Ou S, Kakutani LM, Keeffe JR, Wu HJ, Howarth M, West AP, Barnes CO, Nussenzweig MC, Bjorkman PJ. Mosaic nanoparticles elicit cross-reactive immune responses to zoonotic coronaviruses in mice. Science 2021; 371:735-741. [PMID: 33436524 PMCID: PMC7928838 DOI: 10.1126/science.abf6840] [Citation(s) in RCA: 275] [Impact Index Per Article: 91.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/07/2021] [Indexed: 12/14/2022]
Abstract
Protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and SARS-related emergent zoonotic coronaviruses is urgently needed. We made homotypic nanoparticles displaying the receptor binding domain (RBD) of SARS-CoV-2 or co-displaying SARS-CoV-2 RBD along with RBDs from animal betacoronaviruses that represent threats to humans (mosaic nanoparticles with four to eight distinct RBDs). Mice immunized with RBD nanoparticles, but not soluble antigen, elicited cross-reactive binding and neutralization responses. Mosaic RBD nanoparticles elicited antibodies with superior cross-reactive recognition of heterologous RBDs relative to sera from immunizations with homotypic SARS-CoV-2-RBD nanoparticles or COVID-19 convalescent human plasmas. Moreover, after priming, sera from mosaic RBD-immunized mice neutralized heterologous pseudotyped coronaviruses as well as or better than sera from homotypic SARS-CoV-2-RBD nanoparticle immunizations, demonstrating no loss of immunogenicity against particular RBDs resulting from co-display. A single immunization with mosaic RBD nanoparticles provides a potential strategy to simultaneously protect against SARS-CoV-2 and emerging zoonotic coronaviruses.
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Affiliation(s)
- Alexander A Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Yu E Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Pauline R Hoffman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Susan Ou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Leesa M Kakutani
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hung-Jen Wu
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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127
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Nakata M, Kreikemeyer B. Genetics, Structure, and Function of Group A Streptococcal Pili. Front Microbiol 2021; 12:616508. [PMID: 33633705 PMCID: PMC7900414 DOI: 10.3389/fmicb.2021.616508] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/18/2021] [Indexed: 12/12/2022] Open
Abstract
Streptococcus pyogenes (Group A Streptococcus; GAS) is an exclusively human pathogen. This bacterial species is responsible for a large variety of infections, ranging from purulent but mostly self-limiting oropharynx/skin diseases to streptococcal sequelae, including glomerulonephritis and rheumatic fever, as well as life-threatening streptococcal toxic-shock syndrome. GAS displays a wide array of surface proteins, with antigenicity of the M protein and pili utilized for M- and T-serotyping, respectively. Since the discovery of GAS pili in 2005, their genetic features, including regulation of expression, and structural features, including assembly mechanisms and protein conformation, as well as their functional role in GAS pathogenesis have been intensively examined. Moreover, their potential as vaccine antigens has been studied in detail. Pilus biogenesis-related genes are located in a discrete section of the GAS genome encoding fibronectin and collagen binding proteins and trypsin-resistant antigens (FCT region). Based on the heterogeneity of genetic composition and DNA sequences, this region is currently classified into nine distinguishable forms. Pili and fibronectin-binding proteins encoded in the FCT region are known to be correlated with infection sites, such as the skin and throat, possibly contributing to tissue tropism. As also found for pili of other Gram-positive bacterial pathogens, GAS pilin proteins polymerize via isopeptide bonds, while intramolecular isopeptide bonds present in the pilin provide increased resistance to degradation by proteases. As supported by findings showing that the main subunit is primarily responsible for T-serotyping antigenicity, pilus functions and gene expression modes are divergent. GAS pili serve as adhesins for tonsillar tissues and keratinocyte cell lines. Of note, a minor subunit is considered to have a harpoon function by which covalent thioester bonds with host ligands are formed. Additionally, GAS pili participate in biofilm formation and evasion of the immune system in a serotype/strain-specific manner. These multiple functions highlight crucial roles of pili during the onset of GAS infection. This review summarizes the current state of the art regarding GAS pili, including a new mode of host-GAS interaction mediated by pili, along with insights into pilus expression in terms of tissue tropism.
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Affiliation(s)
- Masanobu Nakata
- Department of Oral Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology and Hygiene, University of Rostock, Rostock, Germany
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128
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Hentrich C, Kellmann SJ, Putyrski M, Cavada M, Hanuschka H, Knappik A, Ylera F. Periplasmic expression of SpyTagged antibody fragments enables rapid modular antibody assembly. Cell Chem Biol 2021; 28:813-824.e6. [PMID: 33529581 DOI: 10.1016/j.chembiol.2021.01.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/16/2020] [Accepted: 01/06/2021] [Indexed: 12/15/2022]
Abstract
Antibodies are essential tools in research and diagnostics. Although antibody fragments typically obtained from in vitro selection can be rapidly produced in bacteria, the generation of full-length antibodies or the modification of antibodies with probes is time and labor intensive. Protein ligation such as SpyTag technology could covalently attach domains and labels to antibody fragments equipped with a SpyTag. However, we found that the established periplasmic expression of antibody fragments in E. coli led to quantitative cleavage of the SpyTag by the proteases Tsp and OmpT. Here we report successful periplasmic expression of SpyTagged Fab fragments and demonstrate the coupling to separately prepared SpyCatcher modules. We used this modular toolbox of SpyCatcher proteins to generate reagents for a variety of immunoassays and measured their performance in comparison with traditional reagents. Furthermore, we demonstrate surface immobilization, high-throughput screening of antibody libraries, and rapid prototyping of antibodies based on modular antibody assembly.
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Affiliation(s)
| | | | - Mateusz Putyrski
- Bio-Rad AbD Serotec GmbH, Zeppelinstraße 4, 82178 Puchheim, Germany
| | - Manuel Cavada
- Bio-Rad AbD Serotec GmbH, Zeppelinstraße 4, 82178 Puchheim, Germany
| | - Hanh Hanuschka
- Bio-Rad AbD Serotec GmbH, Zeppelinstraße 4, 82178 Puchheim, Germany
| | - Achim Knappik
- Bio-Rad AbD Serotec GmbH, Zeppelinstraße 4, 82178 Puchheim, Germany
| | - Francisco Ylera
- Bio-Rad AbD Serotec GmbH, Zeppelinstraße 4, 82178 Puchheim, Germany.
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129
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Scheu AHA, Lim SYT, Metzner FJ, Mohammed S, Howarth M. NeissLock provides an inducible protein anhydride for covalent targeting of endogenous proteins. Nat Commun 2021; 12:717. [PMID: 33514717 PMCID: PMC7846742 DOI: 10.1038/s41467-021-20963-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/04/2021] [Indexed: 11/22/2022] Open
Abstract
The Neisseria meningitidis protein FrpC contains a self-processing module (SPM) undergoing autoproteolysis via an aspartic anhydride. Herein, we establish NeissLock, using a binding protein genetically fused to SPM. Upon calcium triggering of SPM, the anhydride at the C-terminus of the binding protein allows nucleophilic attack by its target protein, ligating the complex. We establish a computational tool to search the Protein Data Bank, assessing proximity of amines to C-termini. We optimize NeissLock using the Ornithine Decarboxylase/Antizyme complex. Various sites on the target (α-amine or ε-amines) react with the anhydride, but reaction is blocked if the partner does not dock. Ligation is efficient at pH 7.0, with half-time less than 2 min. We arm Transforming Growth Factor-α with SPM, enabling specific covalent coupling to Epidermal Growth Factor Receptor at the cell-surface. NeissLock harnesses distinctive protein chemistry for high-yield covalent targeting of endogenous proteins, advancing the possibilities for molecular engineering. Covalent conjugation of endogenous protein complexes offers many opportunities for fundamental and clinical research. Based on a bacterial protein domain that forms a reactive anhydride in the presence of Ca2+, the authors here develop a system that enables the covalent capture of endogenous binding partners.
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Affiliation(s)
- Arne H A Scheu
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Sheryl Y T Lim
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Felix J Metzner
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.,Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377, Munich, Germany
| | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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130
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Tan TK, Rijal P, Rahikainen R, Keeble AH, Schimanski L, Hussain S, Harvey R, Hayes JWP, Edwards JC, McLean RK, Martini V, Pedrera M, Thakur N, Conceicao C, Dietrich I, Shelton H, Ludi A, Wilsden G, Browning C, Zagrajek AK, Bialy D, Bhat S, Stevenson-Leggett P, Hollinghurst P, Tully M, Moffat K, Chiu C, Waters R, Gray A, Azhar M, Mioulet V, Newman J, Asfor AS, Burman A, Crossley S, Hammond JA, Tchilian E, Charleston B, Bailey D, Tuthill TJ, Graham SP, Duyvesteyn HME, Malinauskas T, Huo J, Tree JA, Buttigieg KR, Owens RJ, Carroll MW, Daniels RS, McCauley JW, Stuart DI, Huang KYA, Howarth M, Townsend AR. A COVID-19 vaccine candidate using SpyCatcher multimerization of the SARS-CoV-2 spike protein receptor-binding domain induces potent neutralising antibody responses. Nat Commun 2021; 12:542. [PMID: 33483491 PMCID: PMC7822889 DOI: 10.1038/s41467-020-20654-7] [Citation(s) in RCA: 173] [Impact Index Per Article: 57.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/10/2020] [Indexed: 12/18/2022] Open
Abstract
There is need for effective and affordable vaccines against SARS-CoV-2 to tackle the ongoing pandemic. In this study, we describe a protein nanoparticle vaccine against SARS-CoV-2. The vaccine is based on the display of coronavirus spike glycoprotein receptor-binding domain (RBD) on a synthetic virus-like particle (VLP) platform, SpyCatcher003-mi3, using SpyTag/SpyCatcher technology. Low doses of RBD-SpyVLP in a prime-boost regimen induce a strong neutralising antibody response in mice and pigs that is superior to convalescent human sera. We evaluate antibody quality using ACE2 blocking and neutralisation of cell infection by pseudovirus or wild-type SARS-CoV-2. Using competition assays with a monoclonal antibody panel, we show that RBD-SpyVLP induces a polyclonal antibody response that recognises key epitopes on the RBD, reducing the likelihood of selecting neutralisation-escape mutants. Moreover, RBD-SpyVLP is thermostable and can be lyophilised without losing immunogenicity, to facilitate global distribution and reduce cold-chain dependence. The data suggests that RBD-SpyVLP provides strong potential to address clinical and logistic challenges of the COVID-19 pandemic.
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Affiliation(s)
- Tiong Kit Tan
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK.
| | - Pramila Rijal
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
- Centre for Translational Immunology, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Rolle Rahikainen
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Anthony H Keeble
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Lisa Schimanski
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
- Centre for Translational Immunology, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Saira Hussain
- Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ruth Harvey
- Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Jack W P Hayes
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
| | - Jane C Edwards
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
| | | | | | - Miriam Pedrera
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
| | - Nazia Thakur
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
| | | | | | - Holly Shelton
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
| | - Anna Ludi
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
| | | | - Clare Browning
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
| | | | - Dagmara Bialy
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
| | - Sushant Bhat
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
| | | | - Philippa Hollinghurst
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
- Department of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - Matthew Tully
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
| | - Katy Moffat
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
| | - Chris Chiu
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
| | - Ryan Waters
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
| | - Ashley Gray
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
| | - Mehreen Azhar
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
| | | | - Joseph Newman
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
| | - Amin S Asfor
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
| | - Alison Burman
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
| | | | - John A Hammond
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
| | - Elma Tchilian
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
| | | | - Dalan Bailey
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
| | | | - Simon P Graham
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
| | - Tomas Malinauskas
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
| | - Jiandong Huo
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
- Rutherford Appleton Laboratory, Protein Production UK, Research Complex at Harwell, and Rosalind Franklin Institute, Harwell, Didcot, OX11 0FA, UK
| | - Julia A Tree
- National Infection Service, Public Health England, Porton Down, Salisbury, SP4 0JG, UK
| | - Karen R Buttigieg
- National Infection Service, Public Health England, Porton Down, Salisbury, SP4 0JG, UK
| | - Raymond J Owens
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
- Rutherford Appleton Laboratory, Protein Production UK, Research Complex at Harwell, and Rosalind Franklin Institute, Harwell, Didcot, OX11 0FA, UK
| | - Miles W Carroll
- National Infection Service, Public Health England, Porton Down, Salisbury, SP4 0JG, UK
- Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Rodney S Daniels
- Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - John W McCauley
- Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - David I Stuart
- Centre for Translational Immunology, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Kuan-Ying A Huang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
| | - Alain R Townsend
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK.
- Centre for Translational Immunology, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK.
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131
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Zhu J, Ananthaswamy N, Jain S, Batra H, Tang WC, Lewry DA, Richards ML, David SA, Kilgore PB, Sha J, Drelich A, Tseng CTK, Chopra AK, Rao VB. A Universal Bacteriophage T4 Nanoparticle Platform to Design Multiplex SARS-CoV-2 Vaccine Candidates by CRISPR Engineering. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.19.427310. [PMID: 33501450 PMCID: PMC7836120 DOI: 10.1101/2021.01.19.427310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A "universal" vaccine design platform that can rapidly generate multiplex vaccine candidates is critically needed to control future pandemics. Here, using SARS-CoV-2 pandemic virus as a model, we have developed such a platform by CRISPR engineering of bacteriophage T4. A pipeline of vaccine candidates were engineered by incorporating various viral components into appropriate compartments of phage nanoparticle structure. These include: expressible spike genes in genome, spike and envelope epitopes as surface decorations, and nucleocapsid proteins in packaged core. Phage decorated with spike trimers is found to be the most potent vaccine candidate in mouse and rabbit models. Without any adjuvant, this vaccine stimulated robust immune responses, both T H 1 and T H 2 IgG subclasses, blocked virus-receptor interactions, neutralized viral infection, and conferred complete protection against viral challenge. This new type of nanovaccine design framework might allow rapid deployment of effective phage-based vaccines against any emerging pathogen in the future.
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132
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Modular vaccine platform based on the norovirus-like particle. J Nanobiotechnology 2021; 19:25. [PMID: 33468139 PMCID: PMC7815183 DOI: 10.1186/s12951-021-00772-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Virus-like particle (VLP) vaccines have recently emerged as a safe and effective alternative to conventional vaccine technologies. The strong immunogenic effects of VLPs can be harnessed for making vaccines against any pathogen by decorating VLPs with antigens from the pathogen. Producing the antigenic pathogen fragments and the VLP platform separately makes vaccine development rapid and convenient. Here we decorated the norovirus-like particle with two conserved influenza antigens and tested for the immunogenicity of the vaccine candidates in BALB/c mice. RESULTS SpyTagged noro-VLP was expressed with high efficiency in insect cells and purified using industrially scalable methods. Like the native noro-VLP, SpyTagged noro-VLP is stable for months when refrigerated in a physiological buffer. The conserved influenza antigens were produced separately as SpyCatcher fusions in E. coli before covalent conjugation on the surface of noro-VLP. The noro-VLP had a high adjuvant effect, inducing high titers of antibody production against the antigens presented on its surface. CONCLUSIONS The modular noro-VLP vaccine platform presented here offers a rapid, convenient and safe method to present various soluble protein antigens to the immune system for vaccination and antibody production purposes.
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133
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Fougeroux C, Goksøyr L, Idorn M, Soroka V, Myeni SK, Dagil R, Janitzek CM, Søgaard M, Aves KL, Horsted EW, Erdoğan SM, Gustavsson T, Dorosz J, Clemmensen S, Fredsgaard L, Thrane S, Vidal-Calvo EE, Khalifé P, Hulen TM, Choudhary S, Theisen M, Singh SK, Garcia-Senosiain A, Van Oosten L, Pijlman G, Hierzberger B, Domeyer T, Nalewajek BW, Strøbæk A, Skrzypczak M, Andersson LF, Buus S, Buus AS, Christensen JP, Dalebout TJ, Iversen K, Harritshøj LH, Mordmüller B, Ullum H, Reinert LS, de Jongh WA, Kikkert M, Paludan SR, Theander TG, Nielsen MA, Salanti A, Sander AF. Capsid-like particles decorated with the SARS-CoV-2 receptor-binding domain elicit strong virus neutralization activity. Nat Commun 2021; 12:324. [PMID: 33436573 PMCID: PMC7804149 DOI: 10.1038/s41467-020-20251-8] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/23/2020] [Indexed: 01/29/2023] Open
Abstract
The rapid development of a SARS-CoV-2 vaccine is a global priority. Here, we develop two capsid-like particle (CLP)-based vaccines displaying the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein. RBD antigens are displayed on AP205 CLPs through a split-protein Tag/Catcher, ensuring unidirectional and high-density display of RBD. Both soluble recombinant RBD and RBD displayed on CLPs bind the ACE2 receptor with nanomolar affinity. Mice are vaccinated with soluble RBD or CLP-displayed RBD, formulated in Squalene-Water-Emulsion. The RBD-CLP vaccines induce higher levels of serum anti-spike antibodies than the soluble RBD vaccines. Remarkably, one injection with our lead RBD-CLP vaccine in mice elicits virus neutralization antibody titers comparable to those found in patients that had recovered from COVID-19. Following booster vaccinations, the virus neutralization titers exceed those measured after natural infection, at serum dilutions above 1:10,000. Thus, the RBD-CLP vaccine is a highly promising candidate for preventing COVID-19.
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Affiliation(s)
| | - Louise Goksøyr
- AdaptVac Aps, 2970, Hørsholm, Denmark
- Centre for Medical Parasitology at Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, 2200, Copenhagen, Denmark
| | - Manja Idorn
- Department of Biomedicine, Aarhus University, 8000, Aarhus, Denmark
| | | | - Sebenzile K Myeni
- Department of Medical Microbiology, Leiden University Medical Center, ZA, Leiden, 2333, Netherlands
| | - Robert Dagil
- Centre for Medical Parasitology at Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, 2200, Copenhagen, Denmark
- VAR2pharmaceuticals, 2200, Copenhagen, Denmark
| | - Christoph M Janitzek
- Centre for Medical Parasitology at Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, 2200, Copenhagen, Denmark
| | - Max Søgaard
- ExpreS2ion Biotechnologies Aps, 2970, Hørsholm, Denmark
| | - Kara-Lee Aves
- Centre for Medical Parasitology at Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, 2200, Copenhagen, Denmark
| | - Emma W Horsted
- Centre for Medical Parasitology at Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, 2200, Copenhagen, Denmark
| | - Sayit Mahmut Erdoğan
- Centre for Medical Parasitology at Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, 2200, Copenhagen, Denmark
- Turkish Ministry of Agriculture and Forestry, 06800, Ankara, Turkey
| | - Tobias Gustavsson
- Centre for Medical Parasitology at Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, 2200, Copenhagen, Denmark
- VAR2pharmaceuticals, 2200, Copenhagen, Denmark
| | - Jerzy Dorosz
- ExpreS2ion Biotechnologies Aps, 2970, Hørsholm, Denmark
| | | | - Laurits Fredsgaard
- Centre for Medical Parasitology at Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, 2200, Copenhagen, Denmark
| | | | | | - Paul Khalifé
- Centre for Medical Parasitology at Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, 2200, Copenhagen, Denmark
| | - Thomas M Hulen
- Centre for Medical Parasitology at Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, 2200, Copenhagen, Denmark
| | - Swati Choudhary
- Centre for Medical Parasitology at Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, 2200, Copenhagen, Denmark
- VAR2pharmaceuticals, 2200, Copenhagen, Denmark
| | - Michael Theisen
- Centre for Medical Parasitology at Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, 2200, Copenhagen, Denmark
- Department for Congenital Disorders, Statens Serum Institute, 2300, Copenhagen, Denmark
| | - Susheel K Singh
- Centre for Medical Parasitology at Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, 2200, Copenhagen, Denmark
- Department for Congenital Disorders, Statens Serum Institute, 2300, Copenhagen, Denmark
| | - Asier Garcia-Senosiain
- Centre for Medical Parasitology at Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, 2200, Copenhagen, Denmark
- Department for Congenital Disorders, Statens Serum Institute, 2300, Copenhagen, Denmark
| | - Linda Van Oosten
- Department of Plant Sciences, Laboratory of Virology, 6700AA, Wageningen, Netherlands
| | - Gorben Pijlman
- Department of Plant Sciences, Laboratory of Virology, 6700AA, Wageningen, Netherlands
| | | | - Tanja Domeyer
- ExpreS2ion Biotechnologies Aps, 2970, Hørsholm, Denmark
| | | | | | | | | | - Søren Buus
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Danmark
| | - Anette Stryhn Buus
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Danmark
| | - Jan Pravsgaard Christensen
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Danmark
| | - Tim J Dalebout
- Department of Medical Microbiology, Leiden University Medical Center, ZA, Leiden, 2333, Netherlands
| | - Kasper Iversen
- Department of Cardiology, Herlev Hospital, 2730, Herlev, Denmark
| | - Lene H Harritshøj
- Department of Clinical Immunology, Copenhagen University Hospital, 2100, Copenhagen, Denmark
| | - Benjamin Mordmüller
- Universitätsklinikum Tübingen, Institut für Tropenmedizin, 72074, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné, BP 242, Lambaréné, Gabon
| | - Henrik Ullum
- Department of Cardiology, Herlev Hospital, 2730, Herlev, Denmark
| | - Line S Reinert
- Department of Biomedicine, Aarhus University, 8000, Aarhus, Denmark
| | - Willem Adriaan de Jongh
- AdaptVac Aps, 2970, Hørsholm, Denmark
- ExpreS2ion Biotechnologies Aps, 2970, Hørsholm, Denmark
| | - Marjolein Kikkert
- Department of Medical Microbiology, Leiden University Medical Center, ZA, Leiden, 2333, Netherlands
| | - Søren R Paludan
- Department of Biomedicine, Aarhus University, 8000, Aarhus, Denmark
| | - Thor G Theander
- Centre for Medical Parasitology at Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, 2200, Copenhagen, Denmark
| | - Morten A Nielsen
- Centre for Medical Parasitology at Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, 2200, Copenhagen, Denmark.
| | - Ali Salanti
- Centre for Medical Parasitology at Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, 2200, Copenhagen, Denmark
- VAR2pharmaceuticals, 2200, Copenhagen, Denmark
| | - Adam F Sander
- AdaptVac Aps, 2970, Hørsholm, Denmark.
- Centre for Medical Parasitology at Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, 2200, Copenhagen, Denmark.
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134
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Cohen AA, Gnanapragasam PNP, Lee YE, Hoffman PR, Ou S, Kakutani LM, Keeffe JR, Wu HJ, Howarth M, West AP, Barnes CO, Nussenzweig MC, Bjorkman PJ. Mosaic nanoparticles elicit cross-reactive immune responses to zoonotic coronaviruses in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33236016 PMCID: PMC7685334 DOI: 10.1101/2020.11.17.387092] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protection against SARS-CoV-2 and SARS-related emergent zoonotic coronaviruses is urgently needed. We made homotypic nanoparticles displaying the receptor-binding domain (RBD) of SARS-CoV-2 or co-displaying SARS-CoV-2 RBD along with RBDs from animal betacoronaviruses that represent threats to humans (mosaic nanoparticles; 4–8 distinct RBDs). Mice immunized with RBD-nanoparticles, but not soluble antigen, elicited cross-reactive binding and neutralization responses. Mosaic-RBD-nanoparticles elicited antibodies with superior cross-reactive recognition of heterologous RBDs compared to sera from immunizations with homotypic SARS-CoV-2–RBD-nanoparticles or COVID-19 convalescent human plasmas. Moreover, sera from mosaic-RBD–immunized mice neutralized heterologous pseudotyped coronaviruses equivalently or better after priming than sera from homotypic SARS-CoV-2–RBD-nanoparticle immunizations, demonstrating no immunogenicity loss against particular RBDs resulting from co-display. A single immunization with mosaic-RBD-nanoparticles provides a potential strategy to simultaneously protect against SARS-CoV-2 and emerging zoonotic coronaviruses. One sentence summary: Nanoparticle strategy for pan-sarbecovirus vaccine Immunizing with nanoparticles displaying diverse coronavirus RBDs elicits cross-reactive and neutralizing antibody responses.
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Affiliation(s)
- Alexander A Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Yu E Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Pauline R Hoffman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Susan Ou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Leesa M Kakutani
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hung-Jen Wu
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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135
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Rahikainen R, Rijal P, Tan TK, Wu H, Andersson AC, Barrett JR, Bowden TA, Draper SJ, Townsend AR, Howarth M. Overcoming Symmetry Mismatch in Vaccine Nanoassembly through Spontaneous Amidation. Angew Chem Int Ed Engl 2021; 60:321-330. [PMID: 32886840 PMCID: PMC7821241 DOI: 10.1002/anie.202009663] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Indexed: 12/14/2022]
Abstract
Matching of symmetry at interfaces is a fundamental obstacle in molecular assembly. Virus-like particles (VLPs) are important vaccine platforms against pathogenic threats, including Covid-19. However, symmetry mismatch can prohibit vaccine nanoassembly. We established an approach for coupling VLPs to diverse antigen symmetries. SpyCatcher003 enabled efficient VLP conjugation and extreme thermal resilience. Many people had pre-existing antibodies to SpyTag:SpyCatcher but less to the 003 variants. We coupled the computer-designed VLP not only to monomers (SARS-CoV-2) but also to cyclic dimers (Newcastle disease, Lyme disease), trimers (influenza hemagglutinins), and tetramers (influenza neuraminidases). Even an antigen with dihedral symmetry could be displayed. For the global challenge of influenza, SpyTag-mediated display of trimer and tetramer antigens strongly induced neutralizing antibodies. SpyCatcher003 conjugation enables nanodisplay of diverse symmetries towards generation of potent vaccines.
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Affiliation(s)
- Rolle Rahikainen
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
| | - Pramila Rijal
- MRC Human Immunology UnitMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordOX3 9DSUK
| | - Tiong Kit Tan
- MRC Human Immunology UnitMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordOX3 9DSUK
| | - Hung‐Jen Wu
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
| | - Anne‐Marie C. Andersson
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
- Current address: InProTher ApsOle Maaløes Vej 32200KøbenhavnDenmark
| | | | - Thomas A. Bowden
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordOX3 7BNUK
| | | | - Alain R. Townsend
- MRC Human Immunology UnitMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordOX3 9DSUK
| | - Mark Howarth
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
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136
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Rahikainen R, Rijal P, Tan TK, Wu H, Andersson AC, Barrett JR, Bowden TA, Draper SJ, Townsend AR, Howarth M. Overcoming Symmetry Mismatch in Vaccine Nanoassembly through Spontaneous Amidation. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 133:325-334. [PMID: 38504824 PMCID: PMC10947127 DOI: 10.1002/ange.202009663] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Indexed: 11/10/2022]
Abstract
Matching of symmetry at interfaces is a fundamental obstacle in molecular assembly. Virus-like particles (VLPs) are important vaccine platforms against pathogenic threats, including Covid-19. However, symmetry mismatch can prohibit vaccine nanoassembly. We established an approach for coupling VLPs to diverse antigen symmetries. SpyCatcher003 enabled efficient VLP conjugation and extreme thermal resilience. Many people had pre-existing antibodies to SpyTag:SpyCatcher but less to the 003 variants. We coupled the computer-designed VLP not only to monomers (SARS-CoV-2) but also to cyclic dimers (Newcastle disease, Lyme disease), trimers (influenza hemagglutinins), and tetramers (influenza neuraminidases). Even an antigen with dihedral symmetry could be displayed. For the global challenge of influenza, SpyTag-mediated display of trimer and tetramer antigens strongly induced neutralizing antibodies. SpyCatcher003 conjugation enables nanodisplay of diverse symmetries towards generation of potent vaccines.
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Affiliation(s)
- Rolle Rahikainen
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
| | - Pramila Rijal
- MRC Human Immunology UnitMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordOX3 9DSUK
| | - Tiong Kit Tan
- MRC Human Immunology UnitMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordOX3 9DSUK
| | - Hung‐Jen Wu
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
| | - Anne‐Marie C. Andersson
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
- Current address: InProTher ApsOle Maaløes Vej 32200KøbenhavnDenmark
| | | | - Thomas A. Bowden
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordOX3 7BNUK
| | | | - Alain R. Townsend
- MRC Human Immunology UnitMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordOX3 9DSUK
| | - Mark Howarth
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
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Minamihata K, Hamada Y, Kagawa G, Ramadhan W, Higuchi A, Moriyama K, Wakabayashi R, Goto M, Kamiya N. Dual-Functionalizable Streptavidin-SpyCatcher-Fused Protein-Polymer Hydrogels as Scaffolds for Cell Culture. ACS APPLIED BIO MATERIALS 2020; 3:7734-7742. [PMID: 35019513 DOI: 10.1021/acsabm.0c00940] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Hydrogels possessing the ability to control cell functions have great potential as artificial substrates for cell culture. Herein, we report dual-functionalizable protein-polymer hybrid hydrogels prepared by thiol oxidation catalyzed by horseradish peroxidase and a phenolic molecule. A chimera protein of streptavidin (SA) and the SpyCatcher protein, with a cysteine residue at its N-terminus, (C-SA-SC) was constructed and co-cross-linked with thiol-functionalized four-arm polyethylene glycol (PEG-SH) to obtain hydrogels possessing two orthogonal conjugation moieties. Hydrogel formation using C-SA-SC conjugated with biotinylated or SpyTagged functional molecules (premodification strategy) resulted in the formation of hydrogels with a uniform distribution of the functional molecules. Postmodification of the functional molecules of the C-SA-SC hydrogel with biotin or SpyTag could alter the three-dimensional (3D) spatial distribution of the functional molecules within the hydrogels depending on the mode of conjugation (SA/biotin or SpyCatcher/SpyTag), the size of the functional molecules, and the length of time of the modification. NIH-3T3 cells cultured on a C-SA-SC hydrogel, dual-functionalized with a biotinylated-Arg-Gly-Asp-Ser (RGDS) peptide and a basic fibroblast growth factor (bFGF) with SpyTag, showed cell adhesion to the PEG-SH-based hydrogels and cell morphological changes in response to the immobilized RGDS peptide and the bFGF. Moreover, the cells showed higher proliferation on the dual-functionalized C-SA-SC hydrogel than the cells cultured on hydrogels without either the RGDS peptide or the bFGF, demonstrating the benefits of dual-functionalizable hydrogels. The C-SA-SC hydrogel presented in this study is capable of being orthogonally functionalized by two different functional molecules with different 3D distributions of each molecule within the hydrogel and thus has the potential for use as a cell culturing scaffold for creating artificial cellular microstructures.
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Affiliation(s)
- Kosuke Minamihata
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yusei Hamada
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Genki Kagawa
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Wahyu Ramadhan
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Ayato Higuchi
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kousuke Moriyama
- Department of Chemical and Biological Engineering, National Institute of Technology, Sasebo College, Okishin-cho, Sasebo, Nagasaki 857-1193, Japan
| | - Rie Wakabayashi
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Masahiro Goto
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,Division of Biotechnology, Center for Future Chemistry, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Noriho Kamiya
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,Division of Biotechnology, Center for Future Chemistry, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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138
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Wang R, Sun F. The Spy that links: Creation of nonlinear protein architectures and materials using SpyTag/SpyCatcher chemistry. Methods Enzymol 2020; 647:283-301. [PMID: 33482993 DOI: 10.1016/bs.mie.2020.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The peptide/protein pair, SpyTag/SpyCatcher, which is derived from split immunoglobulin-like collagen adhesin domain (CnaB2) from Streptococcus pyogenes, can spontaneously form a stable Lys-Asp isopeptide bond under physiological conditions. This enabling technology- also known as genetically encoded click chemistry owing to its marked efficiency and specificity-has led to a variety of applications in protein engineering, materials science and synthetic biology in recent years. In this chapter, we discuss the use of SpyTag/SpyCatcher chemistry to create nonlinear protein architectures and materials, with emphasis on its role in shaping up topology engineering as an emerging branch of protein engineering. The synthesis of entirely protein-based molecular networks, Spy networks, is highlighted. The protocols for preparing Spy networks and applications thereof are also illustrated.
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Affiliation(s)
- Ri Wang
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, People's Republic of China
| | - Fei Sun
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, People's Republic of China.
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139
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Karimi Baba Ahmadi M, Mohammadi SA, Makvandi M, Mamoueie M, Rahmati M, Wood D. Column-free purification and coating of SpyCatcher protein on ELISA wells generates universal solid support for capturing of SpyTag-fusion protein from the non-purified condition. Protein Expr Purif 2020; 174:105650. [PMID: 32360597 PMCID: PMC7189850 DOI: 10.1016/j.pep.2020.105650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/02/2020] [Accepted: 04/20/2020] [Indexed: 01/22/2023]
Abstract
•Spy Tag-Protein covalent interaction is rapid and specific method for protein immobilization.•Column free purification of SpyCatcher protein enables develop a universal solid support for SpyTag protein purification.•This method is highly simple and applicable to other proteins.
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Affiliation(s)
- Mohammad Karimi Baba Ahmadi
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Seyed Abolghasem Mohammadi
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Manoochehr Makvandi
- Department of Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Morteza Mamoueie
- Department of Animal Science, Ramin Agricultural and Natural Resources University, Ahvaz, Iran
| | - Mohammad Rahmati
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Animal Science, Ramin Agricultural and Natural Resources University, Ahvaz, Iran.
| | - David Wood
- Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 W. Woodruff Ave., Columbus, OH, 43210, USA
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140
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Lieser RM, Yur D, Sullivan MO, Chen W. Site-Specific Bioconjugation Approaches for Enhanced Delivery of Protein Therapeutics and Protein Drug Carriers. Bioconjug Chem 2020; 31:2272-2282. [DOI: 10.1021/acs.bioconjchem.0c00456] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Rachel M. Lieser
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States of America
| | - Daniel Yur
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States of America
| | - Millicent O. Sullivan
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States of America
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States of America
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141
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Abstract
The specific microenvironment that cells reside in fundamentally impacts their broader function in tissues and organs. At its core, this microenvironment is composed of precise arrangements of cells that encourage homotypic and heterotypic cell-cell interactions, biochemical signaling through soluble factors like cytokines, hormones, and autocrine, endocrine, or paracrine secretions, and the local extracellular matrix (ECM) that provides physical support and mechanobiological stimuli, and further regulates biochemical signaling through cell-ECM interactions like adhesions and growth factor sequestering. Each cue provided in the microenvironment dictates cellular behavior and, thus, overall potential to perform tissue and organ specific function. It follows that in order to recapitulate physiological cell responses and develop constructs capable of replacing damaged tissue, we must engineer the cellular microenvironment very carefully. Many great strides have been made toward this goal using various three-dimensional (3D) tissue culture scaffolds and specific media conditions. Among the various 3D biomimetic scaffolds, synthetic hydrogels have emerged as a highly tunable and tissue-like biomaterial well-suited for implantable tissue-engineered constructs. Because many synthetic hydrogel materials are inherently bioinert, they minimize unintentional cell responses and thus are good candidates for long-term implantable grafts, patches, and organs. This review will provide an overview of commonly used biomaterials for forming synthetic hydrogels for tissue engineering applications and techniques for modifying them to with bioactive properties to elicit the desired cell responses.
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Affiliation(s)
- Asli Z Unal
- Department of Biomedical Engineering, Duke University, 101 Science Drive, Campus Box 90281, Durham, North Carolina 27708, United States
| | - Jennifer L West
- Department of Biomedical Engineering, Duke University, 101 Science Drive, Campus Box 90281, Durham, North Carolina 27708, United States
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142
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Keeble AH, Howarth M. Power to the protein: enhancing and combining activities using the Spy toolbox. Chem Sci 2020; 11:7281-7291. [PMID: 33552459 PMCID: PMC7844731 DOI: 10.1039/d0sc01878c] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/30/2020] [Indexed: 12/27/2022] Open
Abstract
Proteins span an extraordinary range of shapes, sizes and functionalities. Therefore generic approaches are needed to overcome this diversity and stream-line protein analysis or application. Here we review SpyTag technology, now used in hundreds of publications or patents, and its potential for detecting and controlling protein behaviour. SpyTag forms a spontaneous and irreversible isopeptide bond upon binding its protein partner SpyCatcher, where both parts are genetically-encoded. New variants of this pair allow reaction at a rate approaching the diffusion limit, while reversible versions allow purification of SpyTagged proteins or tuned dynamic interaction inside cells. Anchoring of SpyTag-linked proteins has been established to diverse nanoparticles or surfaces, including gold, graphene and the air/water interface. SpyTag/SpyCatcher is mechanically stable, so is widely used for investigating protein folding and force sensitivity. A toolbox of scaffolds allows SpyTag-fusions to be assembled into defined multimers, from dimers to 180-mers, or unlimited 1D, 2D or 3D networks. Icosahedral multimers are being evaluated for vaccination against malaria, HIV and cancer. For enzymes, Spy technology has increased resilience, promoted substrate channelling, and assembled hydrogels for continuous flow biocatalysis. Combinatorial increase in functionality has been achieved through modular derivatisation of antibodies, light-emitting diodes or viral vectors. In living cells, SpyTag allowed imaging of protein trafficking, retargeting of CAR-T cell killing, investigation of heart contraction, and control of nucleosome position. The simple genetic encoding and rapid irreversible reaction provide diverse opportunities to enhance protein function. We describe limitations as well as future directions.
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Affiliation(s)
- Anthony H Keeble
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford , OX1 3QU , UK . ; Tel: +44 (0)1865 613200
| | - Mark Howarth
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford , OX1 3QU , UK . ; Tel: +44 (0)1865 613200
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143
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Zhang N, Liu J, Liu Y, Wu WH, Fang J, Da XD, Wang S, Zhang WB. NMR Spectroscopic Studies Reveal the Critical Role of the Isopeptide Bond in Forming the Otherwise Unstable SpyTag-SpyCatcher Mutant Complexes. Biochemistry 2020; 59:2226-2236. [PMID: 32469203 DOI: 10.1021/acs.biochem.0c00287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interplay between protein folding and chemical reaction has been an intriguing subject. In this contribution, we report the study of SpyTag and SpyCatcher reactive mutants using a combination of sodium dodecyl sulfate-polyacrylamide gel electrophoresis, liquid chromatography and mass spectrometry, circular dichroism, and NMR spectroscopy. It was found that the wild-type SpyCatcher is well-folded in solution and docks with SpyTag to form an intermediate that promotes isopeptide bond formation. By contrast, the double mutant SpyCatcherVA is disordered in solution yet remains reactive toward SpyTag, forming a well-folded covalent complex. Control experiments using the catalytically inactive mutants further reveal the critical role of the isopeptide bond in stabilizing the otherwise loose SpyTag-SpyCatcherVA complex, amplifying the effect of the minute sequence disparity. We believe that the synergy between protein folding and isopeptide bonding is an effective way to enhance protein stability and engineer protein-protein interactions.
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Affiliation(s)
- Nan Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China.,Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, Peking University, Beijing 100871, P. R. China
| | - Jing Liu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China.,Beijing NMR Center, Peking University, Beijing 100871, P. R. China
| | - Yajie Liu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China.,Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, Peking University, Beijing 100871, P. R. China
| | - Wen-Hao Wu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China.,Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, Peking University, Beijing 100871, P. R. China
| | - Jing Fang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China.,Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, Peking University, Beijing 100871, P. R. China
| | - Xiao-Di Da
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China.,Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, Peking University, Beijing 100871, P. R. China
| | - Shenlin Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China.,Beijing NMR Center, Peking University, Beijing 100871, P. R. China
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China.,Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, Peking University, Beijing 100871, P. R. China
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144
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Zhang F, Zhang W. Encrypting Chemical Reactivity in Protein Sequences toward
Information‐Coded
Reactions
†. CHINESE J CHEM 2020. [DOI: 10.1002/cjoc.202000083] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Fan Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 China
| | - Wen‐Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 China
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145
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Affiliation(s)
- Fei Sun
- Department of Chemical and Biological EngineeringThe Hong Kong University of Science and Technology, Clear Water Bay Kowloon Hong Kong SAR China
| | - Wen‐Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of EducationCenter for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 China
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146
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Aves KL, Goksøyr L, Sander AF. Advantages and Prospects of Tag/Catcher Mediated Antigen Display on Capsid-Like Particle-Based Vaccines. Viruses 2020; 12:v12020185. [PMID: 32041299 PMCID: PMC7077247 DOI: 10.3390/v12020185] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 02/03/2020] [Accepted: 02/04/2020] [Indexed: 12/15/2022] Open
Abstract
Capsid-like particles (CLPs) are multimeric, repetitive assemblies of recombinant viral capsid proteins, which are highly immunogenic due to their structural similarity to wild-type viruses. CLPs can be used as molecular scaffolds to enable the presentation of soluble vaccine antigens in a similar structural format, which can significantly increase the immunogenicity of the antigen. CLP-based antigen display can be obtained by various genetic and modular conjugation methods. However, these vary in their versatility as well as efficiency in achieving an immunogenic antigen display. Here, we make a comparative review of the major CLP-based antigen display technologies. The Tag/Catcher-AP205 platform is highlighted as a particularly versatile and efficient technology that offers new qualitative and practical advantages in designing modular CLP vaccines. Finally, we discuss how split-protein Tag/Catcher conjugation systems can help to further propagate and enhance modular CLP vaccine designs.
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Affiliation(s)
- Kara-Lee Aves
- Faculty of Health Science, Institute for Immunology and Microbiology, University of Copenhagen, 2200 Copenhagen, Denmark; (K.-L.A.); (L.G.)
| | - Louise Goksøyr
- Faculty of Health Science, Institute for Immunology and Microbiology, University of Copenhagen, 2200 Copenhagen, Denmark; (K.-L.A.); (L.G.)
- AdaptVac Aps, Agern Alle 1, 2970 Hørsholm, Denmark
| | - Adam F. Sander
- Faculty of Health Science, Institute for Immunology and Microbiology, University of Copenhagen, 2200 Copenhagen, Denmark; (K.-L.A.); (L.G.)
- AdaptVac Aps, Agern Alle 1, 2970 Hørsholm, Denmark
- Correspondence:
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