1
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Bhattacharya S, Jenkins MC, Keshavarz-Joud P, Bourque AR, White K, Alvarez Barkane AM, Bryksin AV, Hernandez C, Kopylov M, Finn MG. Heterologous Prime-Boost with Immunologically Orthogonal Protein Nanoparticles for Peptide Immunofocusing. ACS NANO 2024; 18:20083-20100. [PMID: 39041587 DOI: 10.1021/acsnano.4c00949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Protein nanoparticles are effective platforms for antigen presentation and targeting effector immune cells in vaccine development. Encapsulins are a class of protein-based microbial nanocompartments that self-assemble into icosahedral structures with external diameters ranging from 24 to 42 nm. Encapsulins from Myxococcus xanthus were designed to package bacterial RNA when produced in E. coli and were shown to have immunogenic and self-adjuvanting properties enhanced by this RNA. We genetically incorporated a 20-mer peptide derived from a mutant strain of the SARS-CoV-2 receptor binding domain (RBD) into the encapsulin protomeric coat protein for presentation on the exterior surface of the particle, inducing the formation of several nonicosahedral structures that were characterized by cryogenic electron microscopy. This immunogen elicited conformationally relevant humoral responses to the SARS-CoV-2 RBD. Immunological recognition was enhanced when the same peptide was presented in a heterologous prime/boost vaccination strategy using the engineered encapsulin and a previously reported variant of the PP7 virus-like particle, leading to the development of a selective antibody response against a SARS-CoV-2 RBD point mutant. While generating epitope-focused antibody responses is an interplay between inherent vaccine properties and B/T cells, here we demonstrate the use of orthogonal nanoparticles to fine-tune the control of epitope focusing.
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Affiliation(s)
- Sonia Bhattacharya
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Matthew C Jenkins
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Parisa Keshavarz-Joud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Alisyn Retos Bourque
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Keiyana White
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Amina Maria Alvarez Barkane
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anton V Bryksin
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Carolina Hernandez
- New York Structural Biology Center, New York, New York 10027, United States
| | - Mykhailo Kopylov
- New York Structural Biology Center, New York, New York 10027, United States
| | - M G Finn
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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2
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Helalat SH, Téllez RC, Dezfouli EA, Sun Y. Sortase A-Based Post-translational Modifications on Encapsulin Nanocompartments. Biomacromolecules 2024; 25:2762-2769. [PMID: 38689446 DOI: 10.1021/acs.biomac.3c01415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Protein-based encapsulin nanocompartments, known for their well-defined structures and versatile functionalities, present promising opportunities in the fields of biotechnology and nanomedicine. In this investigation, we effectively developed a sortase A-mediated protein ligation system in Escherichia coli to site-specifically attach target proteins to encapsulin, both internally and on its surfaces without any further in vitro steps. We explored the potential applications of fusing sortase enzyme and a protease for post-translational ligation of encapsulin to a green fluorescent protein and anti-CD3 scFv. Our results demonstrated that this system could attach other proteins to the nanoparticles' exterior surfaces without adversely affecting their folding and assembly processes. Additionally, this system enabled the attachment of proteins inside encapsulins which varied shapes and sizes of the nanoparticles due to cargo overload. This research developed an alternative enzymatic ligation method for engineering encapsulin nanoparticles to facilitate the conjugation process.
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Affiliation(s)
- Seyed Hossein Helalat
- Department of Health Technology, Technical University of Denmark, Ørsteds Plads, DK-2800 Kgs. Lyngby, Denmark
| | - Rodrigo Coronel Téllez
- Department of Health Technology, Technical University of Denmark, Ørsteds Plads, DK-2800 Kgs. Lyngby, Denmark
| | - Ehsan Ansari Dezfouli
- Department of Health Technology, Technical University of Denmark, Ørsteds Plads, DK-2800 Kgs. Lyngby, Denmark
| | - Yi Sun
- Department of Health Technology, Technical University of Denmark, Ørsteds Plads, DK-2800 Kgs. Lyngby, Denmark
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3
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Bhattacharya S, Jenkins MC, Keshavarz-Joud P, Bourque AR, White K, Alvarez Barkane AM, Bryksin AV, Hernandez C, Kopylov M, Finn MG. Heterologous Prime-Boost with Immunologically Orthogonal Protein Nanoparticles for Peptide Immunofocusing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.24.581861. [PMID: 38464232 PMCID: PMC10925081 DOI: 10.1101/2024.02.24.581861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Protein nanoparticles are effective platforms for antigen presentation and targeting effector immune cells in vaccine development. Encapsulins are a class of protein-based microbial nanocompartments that self-assemble into icosahedral structures with external diameters ranging from 24 to 42 nm. Encapsulins from Mxyococcus xanthus were designed to package bacterial RNA when produced in E. coli and were shown to have immunogenic and self-adjuvanting properties enhanced by this RNA. We genetically incorporated a 20-mer peptide derived from a mutant strain of the SARS-CoV-2 receptor binding domain (RBD) into the encapsulin protomeric coat protein for presentation on the exterior surface of the particle. This immunogen elicited conformationally-relevant humoral responses to the SARS-CoV-2 RBD. Immunological recognition was enhanced when the same peptide was presented in a heterologous prime/boost vaccination strategy using the engineered encapsulin and a previously reported variant of the PP7 virus-like particle, leading to the development of a selective antibody response against a SARS-CoV-2 RBD point mutant. While generating epitope-focused antibody responses is an interplay between inherent vaccine properties and B/T cells, here we demonstrate the use of orthogonal nanoparticles to fine-tune the control of epitope focusing.
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Affiliation(s)
- Sonia Bhattacharya
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Matthew C Jenkins
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Parisa Keshavarz-Joud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alisyn Retos Bourque
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Keiyana White
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Amina M Alvarez Barkane
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Anton V Bryksin
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | | | - Mykhailo Kopylov
- New York Structural Biology Center, New York, New York, 10027, USA
| | - M G Finn
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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4
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Sigmund F, Berezin O, Beliakova S, Magerl B, Drawitsch M, Piovesan A, Gonçalves F, Bodea SV, Winkler S, Bousraou Z, Grosshauser M, Samara E, Pujol-Martí J, Schädler S, So C, Irsen S, Walch A, Kofler F, Piraud M, Kornfeld J, Briggman K, Westmeyer GG. Genetically encoded barcodes for correlative volume electron microscopy. Nat Biotechnol 2023; 41:1734-1745. [PMID: 37069313 PMCID: PMC10713455 DOI: 10.1038/s41587-023-01713-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 02/14/2023] [Indexed: 04/19/2023]
Abstract
While genetically encoded reporters are common for fluorescence microscopy, equivalent multiplexable gene reporters for electron microscopy (EM) are still scarce. Here, by installing a variable number of fixation-stable metal-interacting moieties in the lumen of encapsulin nanocompartments of different sizes, we developed a suite of spherically symmetric and concentric barcodes (EMcapsulins) that are readable by standard EM techniques. Six classes of EMcapsulins could be automatically segmented and differentiated. The coding capacity was further increased by arranging several EMcapsulins into distinct patterns via a set of rigid spacers of variable length. Fluorescent EMcapsulins were expressed to monitor subcellular structures in light and EM. Neuronal expression in Drosophila and mouse brains enabled the automatic identification of genetically defined cells in EM. EMcapsulins are compatible with transmission EM, scanning EM and focused ion beam scanning EM. The expandable palette of genetically controlled EM-readable barcodes can augment anatomical EM images with multiplexed gene expression maps.
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Affiliation(s)
- Felix Sigmund
- Munich Institute of Biomedical Engineering, Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine, Technical University of Munich, Munich, Germany
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
| | - Oleksandr Berezin
- Munich Institute of Biomedical Engineering, Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine, Technical University of Munich, Munich, Germany
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
| | - Sofia Beliakova
- Munich Institute of Biomedical Engineering, Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine, Technical University of Munich, Munich, Germany
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
| | - Bernhard Magerl
- Munich Institute of Biomedical Engineering, Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine, Technical University of Munich, Munich, Germany
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
| | - Martin Drawitsch
- Research Group, Circuits of Birdsong, Max Planck Institute for Biological Intelligence, Martinsried, Germany
| | - Alberto Piovesan
- Munich Institute of Biomedical Engineering, Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine, Technical University of Munich, Munich, Germany
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
| | - Filipa Gonçalves
- Munich Institute of Biomedical Engineering, Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine, Technical University of Munich, Munich, Germany
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
| | - Silviu-Vasile Bodea
- Munich Institute of Biomedical Engineering, Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine, Technical University of Munich, Munich, Germany
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
| | - Stefanie Winkler
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
| | - Zoe Bousraou
- Munich Institute of Biomedical Engineering, Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine, Technical University of Munich, Munich, Germany
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
| | - Martin Grosshauser
- Munich Institute of Biomedical Engineering, Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine, Technical University of Munich, Munich, Germany
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
| | - Eleni Samara
- Department Circuits-Computation-Models, Max Planck Institute for Biological Intelligence, Martinsried, Germany
| | - Jesús Pujol-Martí
- Department Circuits-Computation-Models, Max Planck Institute for Biological Intelligence, Martinsried, Germany
| | | | - Chun So
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, Goettingen, Germany
| | - Stephan Irsen
- Max Planck Institute for Neurobiology of Behavior-caesar (MPINB), Bonn, Germany
| | - Axel Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | | | - Marie Piraud
- Helmholtz AI, Helmholtz Munich, Neuherberg, Germany
| | - Joergen Kornfeld
- Research Group, Circuits of Birdsong, Max Planck Institute for Biological Intelligence, Martinsried, Germany
| | - Kevin Briggman
- Max Planck Institute for Neurobiology of Behavior-caesar (MPINB), Bonn, Germany
| | - Gil Gregor Westmeyer
- Munich Institute of Biomedical Engineering, Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine, Technical University of Munich, Munich, Germany.
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany.
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5
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Quinton AR, McDowell HB, Hoiczyk E. Encapsulins: Nanotechnology's future in a shell. ADVANCES IN APPLIED MICROBIOLOGY 2023; 125:1-48. [PMID: 38783722 DOI: 10.1016/bs.aambs.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Encapsulins, virus capsid-like bacterial nanocompartments have emerged as promising tools in medicine, imaging, and material sciences. Recent work has shown that these protein-bound icosahedral 'organelles' possess distinct properties that make them exceptionally usable for nanotechnology applications. A key factor contributing to their appeal is their ability to self-assemble, coupled with their capacity to encapsulate a wide range of cargos. Their genetic manipulability, stability, biocompatibility, and nano-size further enhance their utility, offering outstanding possibilities for practical biotechnology applications. In particular, their amenability to engineering has led to their extensive modification, including the packaging of non-native cargos and the utilization of the shell surface for displaying immunogenic or targeting proteins and peptides. This inherent versatility, combined with the ease of expressing encapsulins in heterologous hosts, promises to provide broad usability. Although mostly not yet commercialized, encapsulins have started to demonstrate their vast potential for biotechnology, from drug delivery to biofuel production and the synthesis of valuable inorganic materials. In this review, we will initially discuss the structure, function and diversity of encapsulins, which form the basis for these emerging applications, before reviewing ongoing practical uses and highlighting promising applications in medicine, engineering and environmental sciences.
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Affiliation(s)
- Amy Ruth Quinton
- School of Biosciences, The Krebs Institute, The University of Sheffield, Sheffield, United Kingdom
| | - Harry Benjamin McDowell
- School of Biosciences, The Krebs Institute, The University of Sheffield, Sheffield, United Kingdom
| | - Egbert Hoiczyk
- School of Biosciences, The Krebs Institute, The University of Sheffield, Sheffield, United Kingdom.
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6
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Gabashvili AN, Chmelyuk NS, Oda VV, Leonova MK, Sarkisova VA, Lazareva PA, Semkina AS, Belyakov NA, Nizamov TR, Nikitin PI. Magnetic and Fluorescent Dual-Labeled Genetically Encoded Targeted Nanoparticles for Malignant Glioma Cell Tracking and Drug Delivery. Pharmaceutics 2023; 15:2422. [PMID: 37896182 PMCID: PMC10609955 DOI: 10.3390/pharmaceutics15102422] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Human glioblastoma multiforme (GBM) is a primary malignant brain tumor, a radically incurable disease characterized by rapid growth resistance to classical therapies, with a median patient survival of about 15 months. For decades, a plethora of approaches have been developed to make GBM therapy more precise and improve the diagnosis of this pathology. Targeted delivery mediated by the use of various molecules (monoclonal antibodies, ligands to overexpressed tumor receptors) is one of the promising methods to achieve this goal. Here we present a novel genetically encoded nanoscale dual-labeled system based on Quasibacillus thermotolerans (Qt) encapsulins exploiting biologically inspired designs with iron-containing nanoparticles as a cargo, conjugated with human fluorescent labeled transferrin (Tf) acting as a vector. It is known that the expression of transferrin receptors (TfR) in glioma cells is significantly higher compared to non-tumor cells, which enables the targeting of the resulting nanocarrier. The selectivity of binding of the obtained nanosystem to glioma cells was studied by qualitative and quantitative assessment of the accumulation of intracellular iron, as well as by magnetic particle quantification method and laser scanning confocal microscopy. Used approaches unambiguously demonstrated that transferrin-conjugated encapsulins were captured by glioma cells much more efficiently than by benign cells. The resulting bioinspired nanoplatform can be supplemented with a chemotherapeutic drug or genotherapeutic agent and used for targeted delivery of a therapeutic agent to malignant glioma cells. Additionally, the observed cell-assisted biosynthesis of magnetic nanoparticles could be an attractive way to achieve a narrow size distribution of particles for various applications.
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Affiliation(s)
- Anna N. Gabashvili
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov Street, 119991 Moscow, Russia; (A.N.G.)
| | - Nelly S. Chmelyuk
- Laboratory “Biomedical Nanomaterials”, National University of Science and Technology “MISIS”, Leninskiy Prospekt 4, 119049 Moscow, Russia
- Department of Medical Nanobiotechnology, Pirogov Russian National Research Medical University, 1 Ostrovityanova Street, 117997 Moscow, Russia; (P.A.L.)
| | - Vera V. Oda
- MILLAB Group Ltd., 100/2 Dmitrovskoe Highway, 127247 Moscow, Russia
| | - Maria K. Leonova
- Department of Physical Chemistry, National University of Science and Technology “MISIS”, Leninskiy Prospekt 4, 119049 Moscow, Russia
| | - Viktoria A. Sarkisova
- Biology Faculty, Lomonosov Moscow State University, 1 Leninskiy Gory, 119234 Moscow, Russia
- Cell Proliferation Laboratory, Engelhardt Institute of Molecular Biology RAS, 32 Vavilov Street, 119991 Moscow, Russia
| | - Polina A. Lazareva
- Department of Medical Nanobiotechnology, Pirogov Russian National Research Medical University, 1 Ostrovityanova Street, 117997 Moscow, Russia; (P.A.L.)
| | - Alevtina S. Semkina
- Department of Medical Nanobiotechnology, Pirogov Russian National Research Medical University, 1 Ostrovityanova Street, 117997 Moscow, Russia; (P.A.L.)
- Department of Basic and Applied Neurobiology, Serbsky National Medical Research Center for Psychiatry and Narcology, 23 Kropotkinskiy Lane, 119991 Moscow, Russia
| | - Nikolai A. Belyakov
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov Street, 119991 Moscow, Russia; (A.N.G.)
| | - Timur R. Nizamov
- Laboratory “Biomedical Nanomaterials”, National University of Science and Technology “MISIS”, Leninskiy Prospekt 4, 119049 Moscow, Russia
| | - Petr I. Nikitin
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov Street, 119991 Moscow, Russia; (A.N.G.)
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7
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Beatty KE, López CS. Characteristics of genetic tags for correlative light and electron microscopy. Curr Opin Chem Biol 2023; 76:102369. [PMID: 37453163 DOI: 10.1016/j.cbpa.2023.102369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/08/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
Fluorescence microscopy is indispensable in live cell studies of fluorescently-labeled proteins, but has limited resolution and context. Electron microscopy offers high-resolution imaging of cellular ultrastructure, including membranes, organelles, and other nanoscale features. However, identifying proteins by EM remains a substantial challenge. There is potential to combine the strengths of both FM and EM through correlative light and EM (CLEM), and bridging the two modalities enables new discoveries and biological insights. CLEM enables cellular proteins to be observed dynamically, across size scales, and in relationship to sub-cellular structures. A central limitation to using CLEM is the scarcity of methods for labeling proteins with CLEM reporters. This review will describe the characteristics of genetic tags for CLEM that are available today, including fixation-resistant fluorescent proteins, 3,3'-diaminobenzidine (DAB)-based tags, metal-chelating tags, DNA origami tags, and VIP tags.
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Affiliation(s)
- Kimberly E Beatty
- Department of Chemical Physiology and Biochemistry Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.
| | - Claudia S López
- Department of Biomedical Engineering Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.
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8
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Song DH, Song CW, Chung J, Jang EH, Kim H, Hur Y, Hur EM, Kim D, Chang JB. In situ silver nanoparticle development for molecular-specific biological imaging via highly accessible microscopies. NANOSCALE ADVANCES 2023; 5:1636-1650. [PMID: 36926569 PMCID: PMC10012848 DOI: 10.1039/d2na00449f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
In biological studies and diagnoses, brightfield (BF), fluorescence, and electron microscopy (EM) are used to image biomolecules inside cells. When compared, their relative advantages and disadvantages are obvious. BF microscopy is the most accessible of the three, but its resolution is limited to a few microns. EM provides a nanoscale resolution, but sample preparation is time-consuming. In this study, we present a new imaging technique, which we termed decoration microscopy (DecoM), and quantitative investigations to address the aforementioned issues in EM and BF microscopy. For molecular-specific EM imaging, DecoM labels proteins inside cells using antibodies bearing 1.4 nm gold nanoparticles (AuNPs) and grows silver layers on the AuNPs' surfaces. The cells are then dried without buffer exchange and imaged using scanning electron microscopy (SEM). Structures labeled with silver-grown AuNPs are clearly visible on SEM, even they are covered with lipid membranes. Using stochastic optical reconstruction microscopy, we show that the drying process causes negligible distortion of structures and that less structural deformation could be achieved through simple buffer exchange to hexamethyldisilazane. Using DecoM, we visualize the nanoscale alterations in microtubules by microtubule-severing proteins that cannot be observed with diffraction-limited fluorescence microscopy. We then combine DecoM with expansion microscopy to enable sub-micron resolution BF microscopy imaging. We first show that silver-grown AuNPs strongly absorb white light, and the structures labeled with them are clearly visible on BF microscopy. We then show that the application of AuNPs and silver development must follow expansion to visualize the labeled proteins clearly with sub-micron resolution.
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Affiliation(s)
- Dae-Hyeon Song
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology Daejeon Korea
| | - Chang Woo Song
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology Daejeon Korea
| | | | - Eun-Hae Jang
- Laboratory of Neuroscience, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University Seoul Korea
| | - Hyunwoo Kim
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology Daejeon Korea
| | - Yongsuk Hur
- BioMedical Research Center, Korea Advanced Institute of Science and Technology Daejeon Korea
| | - Eun-Mi Hur
- Laboratory of Neuroscience, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University Seoul Korea
- BK21 Four Future Veterinary Medicine Leading Education & Research Center, Seoul National University Seoul Korea
| | - Doory Kim
- Department of Chemistry, Hanyang University Seoul Korea
| | - Jae-Byum Chang
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology Daejeon Korea
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9
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Chmelyuk NS, Oda VV, Gabashvili AN, Abakumov MA. Encapsulins: Structure, Properties, and Biotechnological Applications. BIOCHEMISTRY (MOSCOW) 2023; 88:35-49. [PMID: 37068871 PMCID: PMC9937530 DOI: 10.1134/s0006297923010042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
In 1994 a new class of prokaryotic compartments was discovered, collectively called "encapsulins" or "nanocompartments". Encapsulin shell protomer proteins self-assemble to form icosahedral structures of various diameters (24-42 nm). Inside of nanocompartments shells, one or several cargo proteins, diverse in their functions, can be encapsulated. In addition, non-native cargo proteins can be loaded into nanocompartments, and shell surfaces can be modified via various compounds, which makes it possible to create targeted drug delivery systems, labels for optical and MRI imaging, and to use encapsulins as bioreactors. This review describes a number of strategies of encapsulins application in various fields of science, including biomedicine and nanobiotechnologies.
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Affiliation(s)
- Nelly S Chmelyuk
- National University of Science and Technology "MISIS", Moscow, 119049, Russia
- Pirogov Russian National Research Medical University, Ministry of Health of the Russian Federation, Moscow, 117977, Russia
| | - Vera V Oda
- National University of Science and Technology "MISIS", Moscow, 119049, Russia
| | - Anna N Gabashvili
- National University of Science and Technology "MISIS", Moscow, 119049, Russia
| | - Maxim A Abakumov
- National University of Science and Technology "MISIS", Moscow, 119049, Russia.
- Pirogov Russian National Research Medical University, Ministry of Health of the Russian Federation, Moscow, 117977, Russia
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10
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Ross J, McIver Z, Lambert T, Piergentili C, Bird JE, Gallagher KJ, Cruickshank FL, James P, Zarazúa-Arvizu E, Horsfall LE, Waldron KJ, Wilson MD, Mackay CL, Baslé A, Clarke DJ, Marles-Wright J. Pore dynamics and asymmetric cargo loading in an encapsulin nanocompartment. SCIENCE ADVANCES 2022; 8:eabj4461. [PMID: 35080974 PMCID: PMC8791618 DOI: 10.1126/sciadv.abj4461] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
Encapsulins are protein nanocompartments that house various cargo enzymes, including a family of decameric ferritin-like proteins. Here, we study a recombinant Haliangium ochraceum encapsulin:encapsulated ferritin complex using cryo-electron microscopy and hydrogen/deuterium exchange mass spectrometry to gain insight into the structural relationship between the encapsulin shell and its protein cargo. An asymmetric single-particle reconstruction reveals four encapsulated ferritin decamers in a tetrahedral arrangement within the encapsulin nanocompartment. This leads to a symmetry mismatch between the protein cargo and the icosahedral encapsulin shell. The encapsulated ferritin decamers are offset from the interior face of the encapsulin shell. Using hydrogen/deuterium exchange mass spectrometry, we observed the dynamic behavior of the major fivefold pore in the encapsulin shell and show the pore opening via the movement of the encapsulin A-domain. These data will accelerate efforts to engineer the encapsulation of heterologous cargo proteins and to alter the permeability of the encapsulin shell via pore modifications.
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Affiliation(s)
- Jennifer Ross
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Zak McIver
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Thomas Lambert
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - Cecilia Piergentili
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Jasmine Emma Bird
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Kelly J. Gallagher
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - Faye L. Cruickshank
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - Patrick James
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | | | - Louise E. Horsfall
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Kevin J. Waldron
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Marcus D. Wilson
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - C. Logan Mackay
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - Arnaud Baslé
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - David J. Clarke
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - Jon Marles-Wright
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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11
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Boyton I, Goodchild SC, Diaz D, Elbourne A, Collins-Praino LE, Care A. Characterizing the Dynamic Disassembly/Reassembly Mechanisms of Encapsulin Protein Nanocages. ACS OMEGA 2022; 7:823-836. [PMID: 35036749 PMCID: PMC8757444 DOI: 10.1021/acsomega.1c05472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 11/19/2021] [Indexed: 05/22/2023]
Abstract
Encapsulins, self-assembling icosahedral protein nanocages derived from prokaryotes, represent a versatile set of tools for nanobiotechnology. However, a comprehensive understanding of the mechanisms underlying encapsulin self-assembly, disassembly, and reassembly is lacking. Here, we characterize the disassembly/reassembly properties of three encapsulin nanocages that possess different structural architectures: T = 1 (24 nm), T = 3 (32 nm), and T = 4 (42 nm). Using spectroscopic techniques and electron microscopy, encapsulin architectures were found to exhibit varying sensitivities to the denaturant guanidine hydrochloride (GuHCl), extreme pH, and elevated temperature. While all three encapsulins showed the capacity to reassemble following GuHCl-induced disassembly (within 75 min), only the smallest T = 1 nanocage reassembled after disassembly in basic pH (within 15 min). Furthermore, atomic force microscopy revealed that all encapsulins showed a significant loss of structural integrity after undergoing sequential disassembly/reassembly steps. These findings provide insights into encapsulins' disassembly/reassembly dynamics, thus informing their future design, modification, and application.
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Affiliation(s)
- India Boyton
- School
of Life Sciences, University of Technology
Sydney, Ultimo, New South Wales 2007, Australia
- ARC
Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Macquarie
Park, New South Wales 2109, Australia
| | - Sophia C. Goodchild
- Department
of Molecular Sciences, Macquarie University, Macquarie Park, New South
Wales 2109, Australia
| | - Dennis Diaz
- Department
of Molecular Sciences, Macquarie University, Macquarie Park, New South
Wales 2109, Australia
| | - Aaron Elbourne
- School
of Science, College of Science, Engineering and Health, RMIT University, Melbourne, Victoria 3000, Australia
| | - Lyndsey E. Collins-Praino
- Adelaide
Medical School, The University of Adelaide, Adelaide, South Australia 5005, Australia
- ARC
Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Macquarie
Park, New South Wales 2109, Australia
| | - Andrew Care
- School
of Life Sciences, University of Technology
Sydney, Ultimo, New South Wales 2007, Australia
- ARC
Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Macquarie
Park, New South Wales 2109, Australia
- ARC Centre
of Excellence in Synthetic Biology, Macquarie
University, Macquarie Park, New South Wales 2109, Australia
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12
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Michel-Souzy S, Hamelmann NM, Zarzuela-Pura S, Paulusse JMJ, Cornelissen JJLM. Introduction of Surface Loops as a Tool for Encapsulin Functionalization. Biomacromolecules 2021; 22:5234-5242. [PMID: 34747611 PMCID: PMC8672354 DOI: 10.1021/acs.biomac.1c01156] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Encapsulin-based
protein cages are nanoparticles with potential
biomedical applications, such as targeted drug delivery or imaging.
These particles are biocompatible and can be produced in bacteria,
allowing large-scale production and protein engineering. In order
to use these bacterial nanocages in different applications, it is
important to further explore their surface modification and optimize
their production. In this study, we design and show new surface modifications
of Thermotoga maritima (Tm) and Brevibacterium linens (Bl) encapsulins. Two new loops
on the Tm encapsulin with a His-tag insertion after residue 64 and
residue 127 and the modification of the C-terminus on the Bl encapsulin
are reported. The multimodification of the Tm encapsulin enables up
to 240 functionalities on the cage surface, resulting from four potential
modifications per protein subunit. We further report an improved production
protocol giving a better stability and good production yield of the
cages. Finally, we tested the stability of different encapsulin variants
over a year, and the results show a difference in stability arising
from the tag insertion position. These first insights in the structure–property
relationship of encapsulins, with respect to the position of a functional
loop, allow for further study of the use of these protein nanocages
in biomedical applications.
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Affiliation(s)
- Sandra Michel-Souzy
- Department of Molecules and Materials, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands
| | - Naomi M Hamelmann
- Department of Molecules and Materials, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands
| | - Sara Zarzuela-Pura
- Department of Molecules and Materials, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands
| | - Jos M J Paulusse
- Department of Molecules and Materials, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands
| | - Jeroen J L M Cornelissen
- Department of Molecules and Materials, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands
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13
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Almeida AV, Carvalho AJ, Pereira AS. Encapsulin nanocages: Protein encapsulation and iron sequestration. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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14
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Encapsulin Based Self-Assembling Iron-Containing Protein Nanoparticles for Stem Cells MRI Visualization. Int J Mol Sci 2021; 22:ijms222212275. [PMID: 34830156 PMCID: PMC8618560 DOI: 10.3390/ijms222212275] [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: 10/12/2021] [Revised: 11/10/2021] [Accepted: 11/10/2021] [Indexed: 11/16/2022] Open
Abstract
Over the past decade, cell therapy has found many applications in the treatment of different diseases. Some of the cells already used in clinical practice include stem cells and CAR-T cells. Compared with traditional drugs, living cells are much more complicated systems that must be strictly controlled to avoid undesirable migration, differentiation, or proliferation. One of the approaches used to prevent such side effects involves monitoring cell distribution in the human body by any noninvasive technique, such as magnetic resonance imaging (MRI). Long-term tracking of stem cells with artificial magnetic labels, such as magnetic nanoparticles, is quite problematic because such labels can affect the metabolic process and cell viability. Additionally, the concentration of exogenous labels will decrease during cell division, leading to a corresponding decrease in signal intensity. In the current work, we present a new type of genetically encoded label based on encapsulin from Myxococcus xanthus bacteria, stably expressed in human mesenchymal stem cells (MSCs) and coexpressed with ferroxidase as a cargo protein for nanoparticles' synthesis inside encapsulin shells. mZip14 protein was expressed for the enhancement of iron transport into the cell. Together, these three proteins led to the synthesis of iron-containing nanoparticles in mesenchymal stem cells-without affecting cell viability-and increased contrast properties of MSCs in MRI.
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15
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Lohner P, Zmyslia M, Thurn J, Pape JK, Gerasimaitė R, Keller‐Findeisen J, Groeer S, Deuringer B, Süss R, Walther A, Hell SW, Lukinavičius G, Hugel T, Jessen‐Trefzer C. Inside a Shell—Organometallic Catalysis Inside Encapsulin Nanoreactors. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Philipp Lohner
- Department of Pharmaceutical Biology and Biotechnology University of Freiburg Stefan-Meier-Str. 19 79104 Freiburg Germany
| | - Mariia Zmyslia
- Department of Pharmaceutical Biology and Biotechnology University of Freiburg Stefan-Meier-Str. 19 79104 Freiburg Germany
| | - Johann Thurn
- Institute of Physical Chemistry II University of Freiburg Albertstr. 21 79104 Freiburg Germany
| | - Jasmin K. Pape
- Department of NanoBiophotonics Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Goettingen Germany
| | - Rūta Gerasimaitė
- Chromatin Labeling and Imaging Group Department of NanoBiophotonics Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
| | - Jan Keller‐Findeisen
- Department of NanoBiophotonics Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Goettingen Germany
| | - Saskia Groeer
- Institute for Macromolecular Chemistry A3BMS Lab: Adaptive, Active and Autonomous Bioinspired Material Systems University of Freiburg Stefan-Meier-Str. 31, Hermann Staudinger Building 79104 Freiburg Germany
| | - Benedikt Deuringer
- Department of Pharmaceutical Technology and Biopharmacy University of Freiburg Sonnenstraße 5 79104 Freiburg Germany
| | - Regine Süss
- Department of Pharmaceutical Technology and Biopharmacy University of Freiburg Sonnenstraße 5 79104 Freiburg Germany
| | - Andreas Walther
- Cluster of Excellence livMatS @ FIT–Freiburg Center for Interactive Materials and Bioinspired Technologies Georges-Köhler-Allee 105 79110 Freiburg Germany
- Department of Chemistry, A3BMS Lab University of Mainz Duesbergweg 10–14 55128 Mainz Germany
| | - Stefan W. Hell
- Department of NanoBiophotonics Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Goettingen Germany
- Department of Optical Nanoscopy Max Planck Institute for Medical Research Jahnstraße 29 69120 Heidelberg Germany
| | - Gražvydas Lukinavičius
- Chromatin Labeling and Imaging Group Department of NanoBiophotonics Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
| | - Thorsten Hugel
- Institute of Physical Chemistry II University of Freiburg Albertstr. 21 79104 Freiburg Germany
- Cluster of Excellence livMatS @ FIT–Freiburg Center for Interactive Materials and Bioinspired Technologies Georges-Köhler-Allee 105 79110 Freiburg Germany
| | - Claudia Jessen‐Trefzer
- Department of Pharmaceutical Biology and Biotechnology University of Freiburg Stefan-Meier-Str. 19 79104 Freiburg Germany
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16
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Lohner P, Zmyslia M, Thurn J, Pape JK, Gerasimaitė R, Keller‐Findeisen J, Groeer S, Deuringer B, Süss R, Walther A, Hell SW, Lukinavičius G, Hugel T, Jessen‐Trefzer C. Inside a Shell-Organometallic Catalysis Inside Encapsulin Nanoreactors. Angew Chem Int Ed Engl 2021; 60:23835-23841. [PMID: 34418246 PMCID: PMC8596989 DOI: 10.1002/anie.202110327] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Indexed: 01/23/2023]
Abstract
Compartmentalization of chemical reactions inside cells are a fundamental requirement for life. Encapsulins are self-assembling protein-based nanocompartments from the prokaryotic repertoire that present a highly attractive platform for intracellular compartmentalization of chemical reactions by design. Using single-molecule Förster resonance energy transfer and 3D-MINFLUX analysis, we analyze fluorescently labeled encapsulins on a single-molecule basis. Furthermore, by equipping these capsules with a synthetic ruthenium catalyst via covalent attachment to a non-native host protein, we are able to perform in vitro catalysis and go on to show that engineered encapsulins can be used as hosts for transition metal catalysis inside living cells in confined space.
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Affiliation(s)
- Philipp Lohner
- Department of Pharmaceutical Biology and BiotechnologyUniversity of FreiburgStefan-Meier-Str. 1979104FreiburgGermany
| | - Mariia Zmyslia
- Department of Pharmaceutical Biology and BiotechnologyUniversity of FreiburgStefan-Meier-Str. 1979104FreiburgGermany
| | - Johann Thurn
- Institute of Physical Chemistry IIUniversity of FreiburgAlbertstr. 2179104FreiburgGermany
| | - Jasmin K. Pape
- Department of NanoBiophotonicsMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GoettingenGermany
| | - Rūta Gerasimaitė
- Chromatin Labeling and Imaging GroupDepartment of NanoBiophotonicsMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GöttingenGermany
| | - Jan Keller‐Findeisen
- Department of NanoBiophotonicsMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GoettingenGermany
| | - Saskia Groeer
- Institute for Macromolecular ChemistryA3BMS Lab: Adaptive, Active and Autonomous Bioinspired Material SystemsUniversity of FreiburgStefan-Meier-Str. 31, Hermann Staudinger Building79104FreiburgGermany
| | - Benedikt Deuringer
- Department of Pharmaceutical Technology and BiopharmacyUniversity of FreiburgSonnenstraße 579104FreiburgGermany
| | - Regine Süss
- Department of Pharmaceutical Technology and BiopharmacyUniversity of FreiburgSonnenstraße 579104FreiburgGermany
| | - Andreas Walther
- Cluster of Excellence livMatS @ FIT–Freiburg Center for Interactive Materials and Bioinspired TechnologiesGeorges-Köhler-Allee 10579110FreiburgGermany
- Department of Chemistry, A3BMS LabUniversity of MainzDuesbergweg 10–1455128MainzGermany
| | - Stefan W. Hell
- Department of NanoBiophotonicsMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GoettingenGermany
- Department of Optical NanoscopyMax Planck Institute for Medical ResearchJahnstraße 2969120HeidelbergGermany
| | - Gražvydas Lukinavičius
- Chromatin Labeling and Imaging GroupDepartment of NanoBiophotonicsMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GöttingenGermany
| | - Thorsten Hugel
- Institute of Physical Chemistry IIUniversity of FreiburgAlbertstr. 2179104FreiburgGermany
- Cluster of Excellence livMatS @ FIT–Freiburg Center for Interactive Materials and Bioinspired TechnologiesGeorges-Köhler-Allee 10579110FreiburgGermany
| | - Claudia Jessen‐Trefzer
- Department of Pharmaceutical Biology and BiotechnologyUniversity of FreiburgStefan-Meier-Str. 1979104FreiburgGermany
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17
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Schifferer M, Snaidero N, Djannatian M, Kerschensteiner M, Misgeld T. Niwaki Instead of Random Forests: Targeted Serial Sectioning Scanning Electron Microscopy With Reimaging Capabilities for Exploring Central Nervous System Cell Biology and Pathology. Front Neuroanat 2021; 15:732506. [PMID: 34720890 PMCID: PMC8548362 DOI: 10.3389/fnana.2021.732506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/24/2021] [Indexed: 11/13/2022] Open
Abstract
Ultrastructural analysis of discrete neurobiological structures by volume scanning electron microscopy (SEM) often constitutes a "needle-in-the-haystack" problem and therefore relies on sophisticated search strategies. The appropriate SEM approach for a given relocation task not only depends on the desired final image quality but also on the complexity and required accuracy of the screening process. Block-face SEM techniques like Focused Ion Beam or serial block-face SEM are "one-shot" imaging runs by nature and, thus, require precise relocation prior to acquisition. In contrast, "multi-shot" approaches conserve the sectioned tissue through the collection of serial sections onto solid support and allow reimaging. These tissue libraries generated by Array Tomography or Automated Tape Collecting Ultramicrotomy can be screened at low resolution to target high resolution SEM. This is particularly useful if a structure of interest is rare or has been predetermined by correlated light microscopy, which can assign molecular, dynamic and functional information to an ultrastructure. As such approaches require bridging mm to nm scales, they rely on tissue trimming at different stages of sample processing. Relocation is facilitated by endogenous or exogenous landmarks that are visible by several imaging modalities, combined with appropriate registration strategies that allow overlaying images of various sources. Here, we discuss the opportunities of using multi-shot serial sectioning SEM approaches, as well as suitable trimming and registration techniques, to slim down the high-resolution imaging volume to the actual structure of interest and hence facilitate ambitious targeted volume SEM projects.
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Affiliation(s)
- Martina Schifferer
- Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
| | - Nicolas Snaidero
- Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany
- Hertie Institute for Clinical Brain Research, Tübingen, Germany
| | - Minou Djannatian
- Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany
| | - Martin Kerschensteiner
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
- Faculty of Medicine, Biomedical Center (BMC), Ludwig-Maximilians-University Munich, Munich, Germany
| | - Thomas Misgeld
- Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany
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18
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Abstract
Increasing efficiency is an important driving force behind cellular organization and often achieved through compartmentalization. Long recognized as a core principle of eukaryotic cell organization, its widespread occurrence in prokaryotes has only recently come to light. Despite the early discovery of a few microcompartments such as gas vesicles and carboxysomes, the vast majority of these structures in prokaryotes are less than 100 nm in diameter - too small for conventional light microscopy and electron microscopic thin sectioning. Consequently, these smaller-sized nanocompartments have therefore been discovered serendipitously and then through bioinformatics shown to be broadly distributed. Their small uniform size, robust self-assembly, high stability, excellent biocompatibility, and large cargo capacity make them excellent candidates for biotechnology applications. This review will highlight our current knowledge of nanocompartments, the prospects for applications as well as open question and challenges that need to be addressed to fully understand these important structures.
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19
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Van de Steen A, Khalife R, Colant N, Mustafa Khan H, Deveikis M, Charalambous S, Robinson CM, Dabas R, Esteban Serna S, Catana DA, Pildish K, Kalinovskiy V, Gustafsson K, Frank S. Bioengineering bacterial encapsulin nanocompartments as targeted drug delivery system. Synth Syst Biotechnol 2021; 6:231-241. [PMID: 34541345 PMCID: PMC8435816 DOI: 10.1016/j.synbio.2021.09.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/25/2021] [Accepted: 09/01/2021] [Indexed: 11/21/2022] Open
Abstract
The development of Drug Delivery Systems (DDS) has led to increasingly efficient therapies for the treatment and detection of various diseases. DDS use a range of nanoscale delivery platforms produced from polymeric of inorganic materials, such as micelles, and metal and polymeric nanoparticles, but their variant chemical composition make alterations to their size, shape, or structures inherently complex. Genetically encoded protein nanocages are highly promising DDS candidates because of their modular composition, ease of recombinant production in a range of hosts, control over assembly and loading of cargo molecules and biodegradability. One example of naturally occurring nanocompartments are encapsulins, recently discovered bacterial organelles that have been shown to be reprogrammable as nanobioreactors and vaccine candidates. Here we report the design and application of a targeted DDS platform based on the Thermotoga maritima encapsulin reprogrammed to display an antibody mimic protein called Designed Ankyrin repeat protein (DARPin) on the outer surface and to encapsulate a cytotoxic payload. The DARPin9.29 chosen in this study specifically binds to human epidermal growth factor receptor 2 (HER2) on breast cancer cells, as demonstrated in an in vitro cell culture model. The encapsulin-based DDS is assembled in one step in vivo by co-expressing the encapsulin-DARPin9.29 fusion protein with an engineered flavin-binding protein mini-singlet oxygen generator (MiniSOG), from a single plasmid in Escherichia coli. Purified encapsulin-DARPin_miniSOG nanocompartments bind specifically to HER2 positive breast cancer cells and trigger apoptosis, indicating that the system is functional and specific. The DDS is modular and has the potential to form the basis of a multi-receptor targeted system by utilising the DARPin screening libraries, allowing use of new DARPins of known specificities, and through the proven flexibility of the encapsulin cargo loading mechanism, allowing selection of cargo proteins of choice.
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Key Words
- Annexin V-FITC, Annexin V-Fluorescein IsoThiocyanate Conjugate
- Cytotoxic protein
- DARPin
- DARPin9.29, Designed Ankyrin Repeat Protein 9.29
- DDS, Drug Delivery System
- Drug delivery system
- EPR, Enhanced Permeability and Retention effect
- Encapsulin
- HER2, Human Epidermal growth factor Receptor 2
- His6, Hexahistidine
- MSCs, Mesenchymal Stem Cells
- NPs, NanoParticles
- SK-BR-3, Sloan-Kettering Breast cancer cell line/HER2-overexpressing human breast cancer cell line
- STII, StrepII-tag, an eight-residue peptide sequence (Trp-Ser-His-Pro-Gln-Phe-Glu-Lys) with intrinsic affinity toward streptavidin that can be fused to recombinant protein in various fashions
- T. maritima, Thermotoga maritima
- VLPs, Virus-Like Particle
- iGEM, international Genetically Engineered Machine
- iLOV, improved Light, Oxygen or Voltage-sensing flavoprotein
- mScarlet, a bright monomeric red fluorescent protein
- miniSOG, mini-Singlet Oxygen Generator
- rTurboGFP, recombinant Turbo Green Fluorescent Protein
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Affiliation(s)
| | - Rana Khalife
- Department of Biochemical Engineering, University College London, UK
| | - Noelle Colant
- Department of Biochemical Engineering, University College London, UK
| | | | - Matas Deveikis
- Department of Biochemical Engineering, University College London, UK
- UCL iGEM Student Team 2019, UK
| | - Saverio Charalambous
- Department of Biochemical Engineering, University College London, UK
- UCL iGEM Student Team 2019, UK
| | - Clare M. Robinson
- Natural Sciences, University College London, UK
- UCL iGEM Student Team 2019, UK
| | - Rupali Dabas
- Natural Sciences, University College London, UK
- UCL iGEM Student Team 2019, UK
| | - Sofia Esteban Serna
- Division of Biosciences, University College London, UK
- UCL iGEM Student Team 2019, UK
| | - Diana A. Catana
- Division of Biosciences, University College London, UK
- UCL iGEM Student Team 2019, UK
| | - Konstantin Pildish
- Division of Biosciences, University College London, UK
- UCL iGEM Student Team 2019, UK
| | - Vladimir Kalinovskiy
- Division of Biosciences, University College London, UK
- UCL iGEM Student Team 2019, UK
| | - Kenth Gustafsson
- Department of Biochemical Engineering, University College London, UK
| | - Stefanie Frank
- Department of Biochemical Engineering, University College London, UK
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20
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Oerlemans RAJF, Timmermans SBPE, van Hest JCM. Artificial Organelles: Towards Adding or Restoring Intracellular Activity. Chembiochem 2021; 22:2051-2078. [PMID: 33450141 PMCID: PMC8252369 DOI: 10.1002/cbic.202000850] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/15/2021] [Indexed: 12/15/2022]
Abstract
Compartmentalization is one of the main characteristics that define living systems. Creating a physically separated microenvironment allows nature a better control over biological processes, as is clearly specified by the role of organelles in living cells. Inspired by this phenomenon, researchers have developed a range of different approaches to create artificial organelles: compartments with catalytic activity that add new function to living cells. In this review we will discuss three complementary lines of investigation. First, orthogonal chemistry approaches are discussed, which are based on the incorporation of catalytically active transition metal-containing nanoparticles in living cells. The second approach involves the use of premade hybrid nanoreactors, which show transient function when taken up by living cells. The third approach utilizes mostly genetic engineering methods to create bio-based structures that can be ultimately integrated with the cell's genome to make them constitutively active. The current state of the art and the scope and limitations of the field will be highlighted with selected examples from the three approaches.
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Affiliation(s)
- Roy A. J. F. Oerlemans
- Bio-Organic Chemistry Research GroupInstitute for Complex Molecular SystemsEindhoven University of TechnologyP.O. Box 513 (STO3.41)5600 MBEindhovenThe Netherlands
| | - Suzanne B. P. E. Timmermans
- Bio-Organic Chemistry Research GroupInstitute for Complex Molecular SystemsEindhoven University of TechnologyP.O. Box 513 (STO3.41)5600 MBEindhovenThe Netherlands
| | - Jan C. M. van Hest
- Bio-Organic Chemistry Research GroupInstitute for Complex Molecular SystemsEindhoven University of TechnologyP.O. Box 513 (STO3.41)5600 MBEindhovenThe Netherlands
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21
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Rodríguez JM, Allende-Ballestero C, Cornelissen JJLM, Castón JR. Nanotechnological Applications Based on Bacterial Encapsulins. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1467. [PMID: 34206092 PMCID: PMC8229669 DOI: 10.3390/nano11061467] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/23/2021] [Accepted: 05/27/2021] [Indexed: 02/06/2023]
Abstract
Encapsulins are proteinaceous nanocontainers, constructed by a single species of shell protein that self-assemble into 20-40 nm icosahedral particles. Encapsulins are structurally similar to the capsids of viruses of the HK97-like lineage, to which they are evolutionarily related. Nearly all these nanocontainers encase a single oligomeric protein that defines the physiological role of the complex, although a few encapsulate several activities within a single particle. Encapsulins are abundant in bacteria and archaea, in which they participate in regulation of oxidative stress, detoxification, and homeostasis of key chemical elements. These nanocontainers are physically robust, contain numerous pores that permit metabolite flux through the shell, and are very tolerant of genetic manipulation. There are natural mechanisms for efficient functionalization of the outer and inner shell surfaces, and for the in vivo and in vitro internalization of heterologous proteins. These characteristics render encapsulin an excellent platform for the development of biotechnological applications. Here we provide an overview of current knowledge of encapsulin systems, summarize the remarkable toolbox developed by researchers in this field, and discuss recent advances in the biomedical and bioengineering applications of encapsulins.
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Affiliation(s)
- Javier M. Rodríguez
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (J.M.R.); (C.A.-B.)
| | - Carolina Allende-Ballestero
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (J.M.R.); (C.A.-B.)
| | - Jeroen J. L. M. Cornelissen
- Department of Molecules and Materials, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands;
| | - José R. Castón
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (J.M.R.); (C.A.-B.)
- Nanobiotechnology Associated Unit CNB-CSIC-IMDEA, Campus Cantoblanco, 28049 Madrid, Spain
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22
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Farhadi A, Sigmund F, Westmeyer GG, Shapiro MG. Genetically encodable materials for non-invasive biological imaging. NATURE MATERIALS 2021; 20:585-592. [PMID: 33526879 PMCID: PMC8606175 DOI: 10.1038/s41563-020-00883-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 11/18/2020] [Indexed: 05/04/2023]
Abstract
Many questions in basic biology and medicine require the ability to visualize the function of specific cells and molecules inside living organisms. In this context, technologies such as ultrasound, optoacoustics and magnetic resonance provide non-invasive imaging access to deep-tissue regions, as used in many laboratories and clinics to visualize anatomy and physiology. In addition, recent work has enabled these technologies to image the location and function of specific cells and molecules inside the body by coupling the physics of sound waves, nuclear spins and light absorption to unique protein-based materials. These materials, which include air-filled gas vesicles, capsid-like nanocompartments, pigment-producing enzymes and transmembrane transporters, enable new forms of biomolecular and cellular contrast. The ability of these protein-based contrast agents to be genetically encoded and produced by cells creates opportunities for unprecedented in vivo studies of cellular function, while their amenability to genetic engineering enables atomic-level design of their physical, chemical and biological properties.
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Affiliation(s)
- Arash Farhadi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Felix Sigmund
- Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
- Institute for Synthetic Biomedicine, Helmholtz Zentrum Muenchen, Neuherberg, Germany
| | - Gil Gregor Westmeyer
- Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany.
- Institute for Synthetic Biomedicine, Helmholtz Zentrum Muenchen, Neuherberg, Germany.
| | - Mikhail G Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
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23
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Efremova MV, Bodea SV, Sigmund F, Semkina A, Westmeyer GG, Abakumov MA. Genetically Encoded Self-Assembling Iron Oxide Nanoparticles as a Possible Platform for Cancer-Cell Tracking. Pharmaceutics 2021; 13:pharmaceutics13030397. [PMID: 33809789 PMCID: PMC8002387 DOI: 10.3390/pharmaceutics13030397] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/09/2021] [Accepted: 03/12/2021] [Indexed: 01/15/2023] Open
Abstract
The study of growth and possible metastasis in animal models of tumors would benefit from reliable cell labels for noninvasive whole-organism imaging techniques such as magnetic resonance imaging. Genetically encoded cell-tracking reporters have the advantage that they are contrast-selective for viable cells with intact protein expression machinery. Besides, these reporters do not suffer from dilution during cell division. Encapsulins, which are bacterial protein nanocompartments, can serve as genetically controlled labels for multimodal detection of cells. Such nanocompartments can host various guest molecules inside their lumen. These include, for example, fluorescent proteins or enzymes with ferroxidase activity leading to biomineralization of iron oxide inside the encapsulin nanoshell. The aim of this work was to implement heterologous expression of encapsulin systems from Quasibacillus thermotolerans using the fluorescent reporter protein mScarlet-I and ferroxidase IMEF in the human hepatocellular carcinoma cell line HepG2. The successful expression of self-assembled encapsulin nanocompartments with functional cargo proteins was confirmed by fluorescence microscopy and transmission electron microscopy. Also, coexpression of encapsulin nanoshells, ferroxidase cargo, and iron transporter led to an increase in T2-weighted contrast in magnetic resonance imaging of HepG2 cells. The results demonstrate that the encapsulin cargo system from Q. thermotolerans may be suitable for multimodal imaging of cancer cells and could contribute to further in vitro and in vivo studies.
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Affiliation(s)
- Maria V. Efremova
- Department of Chemistry & TUM School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany; (S.-V.B.); (F.S.); (G.G.W.)
- Institute for Synthetic Biomedicine, Helmholtz Center Munich, 85764 Neuherberg, Germany
- Correspondence: (M.V.E.); (M.A.A.); Tel.: +74-95-638-4465 (M.A.A.)
| | - Silviu-Vasile Bodea
- Department of Chemistry & TUM School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany; (S.-V.B.); (F.S.); (G.G.W.)
- Institute for Synthetic Biomedicine, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Felix Sigmund
- Department of Chemistry & TUM School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany; (S.-V.B.); (F.S.); (G.G.W.)
- Institute for Synthetic Biomedicine, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Alevtina Semkina
- Department of Medical Nanobiotechnology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia;
- V.P. Serbskiy National Medical Research Center of Psychiatry and Narcology, 119034 Moscow, Russia
| | - Gil G. Westmeyer
- Department of Chemistry & TUM School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany; (S.-V.B.); (F.S.); (G.G.W.)
- Institute for Synthetic Biomedicine, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Maxim A. Abakumov
- Department of Medical Nanobiotechnology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia;
- Laboratory “Biomedical Nanomaterials”, National University of Science and Technology “MISiS”, 119049 Moscow, Russia
- Correspondence: (M.V.E.); (M.A.A.); Tel.: +74-95-638-4465 (M.A.A.)
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24
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Dhanker R, Hussain T, Tyagi P, Singh KJ, Kamble SS. The Emerging Trend of Bio-Engineering Approaches for Microbial Nanomaterial Synthesis and Its Applications. Front Microbiol 2021; 12:638003. [PMID: 33796089 PMCID: PMC8008120 DOI: 10.3389/fmicb.2021.638003] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 02/15/2021] [Indexed: 12/11/2022] Open
Abstract
Micro-organisms colonized the world before the multi-cellular organisms evolved. With the advent of microscopy, their existence became evident to the mankind and also the vast processes they regulate, that are in direct interest of the human beings. One such process that intrigued the researchers is the ability to grow in presence of toxic metals. The process seemed to be simple with the metal ions being sequestrated into the inclusion bodies or cell surfaces enabling the conversion into nontoxic nanostructures. However, the discovery of genome sequencing techniques highlighted the genetic makeup of these microbes as a quintessential aspect of these phenomena. The findings of metal resistance genes (MRG) in these microbes showed a rather complex regulation of these processes. Since most of these MRGs are plasmid encoded they can be transferred horizontally. With the discovery of nanoparticles and their many applications from polymer chemistry to drug delivery, the demand for innovative techniques of nanoparticle synthesis increased dramatically. It is now established that microbial synthesis of nanoparticles provides numerous advantages over the existing chemical methods. However, it is the explicit use of biotechnology, molecular biology, metabolic engineering, synthetic biology, and genetic engineering tools that revolutionized the world of microbial nanotechnology. Detailed study of the micro and even nanolevel assembly of microbial life also intrigued biologists and engineers to generate molecular motors that mimic bacterial flagellar motor. In this review, we highlight the importance and tremendous hidden potential of bio-engineering tools in exploiting the area of microbial nanoparticle synthesis. We also highlight the application oriented specific modulations that can be done in the stages involved in the synthesis of these nanoparticles. Finally, the role of these nanoparticles in the natural ecosystem is also addressed.
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Affiliation(s)
- Raunak Dhanker
- Department of Basic and Applied Sciences, School of Engineering and Sciences, GD Goenka University, Gurugram, India
| | - Touseef Hussain
- Department of Botany, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Priyanka Tyagi
- Department of Basic and Applied Sciences, School of Engineering and Sciences, GD Goenka University, Gurugram, India
| | - Kawal Jeet Singh
- Amity Institute of Biotechnology, Amity University, Noida, India
| | - Shashank S. Kamble
- Department of Basic and Applied Sciences, School of Engineering and Sciences, GD Goenka University, Gurugram, India
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25
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Diaz D, Vidal X, Sunna A, Care A. Bioengineering a Light-Responsive Encapsulin Nanoreactor: A Potential Tool for In Vitro Photodynamic Therapy. ACS APPLIED MATERIALS & INTERFACES 2021; 13:7977-7986. [PMID: 33586952 DOI: 10.1021/acsami.0c21141] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Encapsulins, a prokaryotic class of self-assembling protein nanocompartments, are being re-engineered to serve as "nanoreactors" for the augmentation or creation of key biochemical reactions. However, approaches that allow encapsulin nanoreactors to be functionally activated with spatial and temporal precision are lacking. We report the construction of a light-responsive encapsulin nanoreactor for "on demand" production of reactive oxygen species (ROS). Herein, encapsulins were loaded with the fluorescent flavoprotein mini-singlet oxygen generator (miniSOG), a biological photosensitizer that is activated by blue light to generate ROS, primarily singlet oxygen (1O2). We established that the nanocompartments stably encased miniSOG and in response to blue light were able to mediate the photoconversion of molecular oxygen into ROS. Using an in vitro model of lung cancer, we showed that ROS generated by the nanoreactor triggered photosensitized oxidation reactions which exerted a toxic effect on tumor cells, suggesting utility in photodynamic therapy. This encapsulin nanoreactor thus represents a platform for the light-controlled initiation and/or modulation of ROS-driven processes in biomedicine and biotechnology.
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Affiliation(s)
- Dennis Diaz
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Xavier Vidal
- Fraunhofer Institut für Angewandte Festkörperphysik (IAF), Tullastrasse 72, 79108 Freiburg, Germany
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
- ARC Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, NSW 2109, Australia
| | - Andrew Care
- ARC Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, NSW 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
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26
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Lei Z, Zhang Y, Liu G. eMIONs: novel genetically engineered nanocages for magnetic hyperthermia cancer therapy. Mol Cell Oncol 2021; 8:1863739. [PMID: 33553611 PMCID: PMC7849714 DOI: 10.1080/23723556.2020.1863739] [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: 11/28/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 10/22/2022]
Abstract
The clinical introduction of magnetic hyperthermia therapy (MHT) has been hindered by current available agents with poor magnetic-to-thermal conversion efficiency and biocompatibility. It is believed that the genetically engineered magnetic nanocages of encapsulin-produced magnetic iron oxide nanocomposites (eMIONs) have great potential as clinically translatable MHT agents for cancer magneto-catalytic theranostics.
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Affiliation(s)
- Zhao Lei
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, China
| | - Yang Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, China
| | - Gang Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, China
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27
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Groaz A, Moghimianavval H, Tavella F, Giessen TW, Vecchiarelli AG, Yang Q, Liu AP. Engineering spatiotemporal organization and dynamics in synthetic cells. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2020; 13:e1685. [PMID: 33219745 DOI: 10.1002/wnan.1685] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 10/13/2020] [Accepted: 10/30/2020] [Indexed: 12/28/2022]
Abstract
Constructing synthetic cells has recently become an appealing area of research. Decades of research in biochemistry and cell biology have amassed detailed part lists of components involved in various cellular processes. Nevertheless, recreating any cellular process in vitro in cell-sized compartments remains ambitious and challenging. Two broad features or principles are key to the development of synthetic cells-compartmentalization and self-organization/spatiotemporal dynamics. In this review article, we discuss the current state of the art and research trends in the engineering of synthetic cell membranes, development of internal compartmentalization, reconstitution of self-organizing dynamics, and integration of activities across scales of space and time. We also identify some research areas that could play a major role in advancing the impact and utility of engineered synthetic cells. This article is categorized under: Biology-Inspired Nanomaterials > Lipid-Based Structures Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.
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Affiliation(s)
| | | | | | | | | | - Qiong Yang
- University of Michigan, Ann Arbor, Michigan, USA
| | - Allen P Liu
- University of Michigan, Ann Arbor, Michigan, USA
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28
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Jones JA, Giessen TW. Advances in encapsulin nanocompartment biology and engineering. Biotechnol Bioeng 2020; 118:491-505. [PMID: 32918485 DOI: 10.1002/bit.27564] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/12/2020] [Accepted: 09/09/2020] [Indexed: 12/23/2022]
Abstract
Compartmentalization is an essential feature of all cells. It allows cells to segregate and coordinate physiological functions in a controlled and ordered manner. Different mechanisms of compartmentalization exist, with the most relevant to prokaryotes being encapsulation via self-assembling protein-based compartments. One widespread example of such is that of encapsulins-cage-like protein nanocompartments able to compartmentalize specific reactions, pathways, and processes in bacteria and archaea. While still relatively nascent bioengineering tools, encapsulins exhibit many promising characteristics, including a number of defined compartment sizes ranging from 24 to 42 nm, straightforward expression, the ability to self-assemble via the Hong Kong 97-like fold, marked physical robustness, and internal and external handles primed for rational genetic and molecular manipulation. Moreover, encapsulins allow for facile and specific encapsulation of native or heterologous cargo proteins via naturally or rationally fused targeting peptide sequences. Taken together, the attributes of encapsulins promise substantial customizability and broad usability. This review discusses recent advances in employing engineered encapsulins across various fields, from their use as bionanoreactors to targeted delivery systems and beyond. A special focus will be provided on the rational engineering of encapsulin systems and their potential promise as biomolecular research tools.
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Affiliation(s)
- Jesse A Jones
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Tobias W Giessen
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA.,Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
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29
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Gabashvili AN, Chmelyuk NS, Efremova MV, Malinovskaya JA, Semkina AS, Abakumov MA. Encapsulins-Bacterial Protein Nanocompartments: Structure, Properties, and Application. Biomolecules 2020; 10:biom10060966. [PMID: 32604934 PMCID: PMC7355545 DOI: 10.3390/biom10060966] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/21/2020] [Accepted: 06/23/2020] [Indexed: 02/07/2023] Open
Abstract
Recently, a new class of prokaryotic compartments, collectively called encapsulins or protein nanocompartments, has been discovered. The shell proteins of these structures self-organize to form icosahedral compartments with a diameter of 25-42 nm, while one or more cargo proteins with various functions can be encapsulated in the nanocompartment. Non-native cargo proteins can be loaded into nanocompartments and the surface of the shells can be further functionalized, which allows for developing targeted drug delivery systems or using encapsulins as contrast agents for magnetic resonance imaging. Since the genes encoding encapsulins can be integrated into the cell genome, encapsulins are attractive for investigation in various scientific fields, including biomedicine and nanotechnology.
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Affiliation(s)
- Anna N. Gabashvili
- Laboratory “Biomedical Nanomaterials”, National University of Science and Technology “MISiS”, Leninskiy Prospect, 4, 119049 Moscow, Russia; (A.N.G.); (N.S.C.)
- Department of Medical Nanobiotechnoilogy, Pirogov Russian National Research Medical University, Ostrovityanova st, 1, 117997 Moscow, Russia;
| | - Nelly S. Chmelyuk
- Laboratory “Biomedical Nanomaterials”, National University of Science and Technology “MISiS”, Leninskiy Prospect, 4, 119049 Moscow, Russia; (A.N.G.); (N.S.C.)
| | - Maria V. Efremova
- Department of Nuclear Medicine, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany;
- Institute of Biological and Medical Imaging and Institute of Developmental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | | | - Alevtina S. Semkina
- Department of Medical Nanobiotechnoilogy, Pirogov Russian National Research Medical University, Ostrovityanova st, 1, 117997 Moscow, Russia;
| | - Maxim A. Abakumov
- Laboratory “Biomedical Nanomaterials”, National University of Science and Technology “MISiS”, Leninskiy Prospect, 4, 119049 Moscow, Russia; (A.N.G.); (N.S.C.)
- Department of Medical Nanobiotechnoilogy, Pirogov Russian National Research Medical University, Ostrovityanova st, 1, 117997 Moscow, Russia;
- Correspondence: ; Tel.: +7-903-586-4777
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30
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Szewczak L. Just Solid or Liquid Enough. Cell 2019; 178:763-765. [PMID: 31398330 DOI: 10.1016/j.cell.2019.07.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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