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Puertas-Bartolomé M, Venegas-Bustos D, Acosta S, Rodríguez-Cabello JC. Contribution of the ELRs to the development of advanced in vitro models. Front Bioeng Biotechnol 2024; 12:1363865. [PMID: 38650751 PMCID: PMC11033926 DOI: 10.3389/fbioe.2024.1363865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 03/18/2024] [Indexed: 04/25/2024] Open
Abstract
Developing in vitro models that accurately mimic the microenvironment of biological structures or processes holds substantial promise for gaining insights into specific biological functions. In the field of tissue engineering and regenerative medicine, in vitro models able to capture the precise structural, topographical, and functional complexity of living tissues, prove to be valuable tools for comprehending disease mechanisms, assessing drug responses, and serving as alternatives or complements to animal testing. The choice of the right biomaterial and fabrication technique for the development of these in vitro models plays an important role in their functionality. In this sense, elastin-like recombinamers (ELRs) have emerged as an important tool for the fabrication of in vitro models overcoming the challenges encountered in natural and synthetic materials due to their intrinsic properties, such as phase transition behavior, tunable biological properties, viscoelasticity, and easy processability. In this review article, we will delve into the use of ELRs for molecular models of intrinsically disordered proteins (IDPs), as well as for the development of in vitro 3D models for regenerative medicine. The easy processability of the ELRs and their rational design has allowed their use for the development of spheroids and organoids, or bioinks for 3D bioprinting. Thus, incorporating ELRs into the toolkit of biomaterials used for the fabrication of in vitro models, represents a transformative step forward in improving the accuracy, efficiency, and functionality of these models, and opening up a wide range of possibilities in combination with advanced biofabrication techniques that remains to be explored.
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Affiliation(s)
- María Puertas-Bartolomé
- Technical Proteins Nanobiotechnology, S.L. (TPNBT), Valladolid, Spain
- Bioforge Lab (Group for Advanced Materials and Nanobiotechnology), CIBER's Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Edificio LUCIA, Universidad de Valladolid, Valladolid, Spain
| | - Desiré Venegas-Bustos
- Bioforge Lab (Group for Advanced Materials and Nanobiotechnology), CIBER's Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Edificio LUCIA, Universidad de Valladolid, Valladolid, Spain
| | - Sergio Acosta
- Bioforge Lab (Group for Advanced Materials and Nanobiotechnology), CIBER's Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Edificio LUCIA, Universidad de Valladolid, Valladolid, Spain
| | - José Carlos Rodríguez-Cabello
- Bioforge Lab (Group for Advanced Materials and Nanobiotechnology), CIBER's Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Edificio LUCIA, Universidad de Valladolid, Valladolid, Spain
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2
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Züblin P, Zeller A, Moulis C, Remaud-Simeon M, Yao Y, Mezzenga R. Expanding the Enzymatic Polymerization Landscape by Lipid Mesophase Soft Nanoconfinement. Angew Chem Int Ed Engl 2024; 63:e202312880. [PMID: 37962302 DOI: 10.1002/anie.202312880] [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: 08/31/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/15/2023]
Abstract
Soft nanoconfinement can increase chemical reactivity in nature and has therefore led to considerable interest in transferring this universal feature to artificial biological systems. However, little is known about the underlying principles of soft nanoconfinement responsible for the enhancement of biochemical reactions. Herein we demonstrate how enzymatic polymerization can be expanded, optimized, and engineered when carried out under soft nanoconfinement mediated by lipidic mesophases. By systematically varying the water content in the mesophase and thus the diameter of the confined water nanochannels, we show higher efficiency, turnover rate, and degrees of polymerization as compared to the bulk aqueous solution, all controlled by soft nanoconfinement effects. Furthermore, we exploit the unique properties of unfreezing soft nanoconfined water to perform the first enzymatic polymerization at -20 °C in pure aqueous media. These results underpin lipidic mesophases as a versatile host system for chemical reactions and promote them as an original and unexplored platform for enzymatic polymerization.
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Affiliation(s)
- Patrick Züblin
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092, Zürich, Switzerland
| | - Adrian Zeller
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092, Zürich, Switzerland
| | - Claire Moulis
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 135 Av. de Rangueil, 31400, Toulouse, France
| | - Magali Remaud-Simeon
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 135 Av. de Rangueil, 31400, Toulouse, France
| | - Yang Yao
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092, Zürich, Switzerland
| | - Raffaele Mezzenga
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092, Zürich, Switzerland
- Department of Materials, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zürich, Switzerland
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3
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Kröll S, Burgahn T, Rabe KS, Franzreb M, Niemeyer CM. Nano- and Microscale Confinements in DNA-Scaffolded Enzyme Cascade Reactions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2304578. [PMID: 37732702 DOI: 10.1002/smll.202304578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/24/2023] [Indexed: 09/22/2023]
Abstract
Artificial reconstruction of naturally evolved principles, such as compartmentalization and cascading of multienzyme complexes, offers enormous potential for the development of biocatalytic materials and processes. Due to their unique addressability at the nanoscale, DNA origami nanostructures (DON) have proven to be an exceptionally powerful tool for studying the fundamental processes in biocatalytic cascades. To systematically investigate the diffusion-reaction network of (co)substrate transfer in enzyme cascades, a model system of stereoselective ketoreductase (KRED) with cofactor regenerating enzyme is assembled in different spatial arrangements on DNA nanostructures and is located in the sphere of microbeads (MB) as a spatially confining nano- and microenvironment, respectively. The results, obtained through the use of highly sensitive analytical methods, Western blot-based quantification of the enzymes, and mass spectrometric (MS) product detection, along with theoretical modeling, provide strong evidence for the presence of two interacting compartments, the diffusion layers around the microbead and the DNA scaffold, which influence the catalytic efficiency of the cascade. It is shown that the microscale compartment exerts a strong influence on the productivity of the cascade, whereas the nanoscale arrangement of enzymes has no influence but can be modulated by the insertion of a diffusion barrier.
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Affiliation(s)
- Sandra Kröll
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Teresa Burgahn
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Kersten S Rabe
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Matthias Franzreb
- Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces (IFG), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
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4
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Boob AG, Chen J, Zhao H. Enabling pathway design by multiplex experimentation and machine learning. Metab Eng 2024; 81:70-87. [PMID: 38040110 DOI: 10.1016/j.ymben.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/01/2023] [Accepted: 11/25/2023] [Indexed: 12/03/2023]
Abstract
The remarkable metabolic diversity observed in nature has provided a foundation for sustainable production of a wide array of valuable molecules. However, transferring the biosynthetic pathway to the desired host often runs into inherent failures that arise from intermediate accumulation and reduced flux resulting from competing pathways within the host cell. Moreover, the conventional trial and error methods utilized in pathway optimization struggle to fully grasp the intricacies of installed pathways, leading to time-consuming and labor-intensive experiments, ultimately resulting in suboptimal yields. Considering these obstacles, there is a pressing need to explore the enzyme expression landscape and identify the optimal pathway configuration for enhanced production of molecules. This review delves into recent advancements in pathway engineering, with a focus on multiplex experimentation and machine learning techniques. These approaches play a pivotal role in overcoming the limitations of traditional methods, enabling exploration of a broader design space and increasing the likelihood of discovering optimal pathway configurations for enhanced production of molecules. We discuss several tools and strategies for pathway design, construction, and optimization for sustainable and cost-effective microbial production of molecules ranging from bulk to fine chemicals. We also highlight major successes in academia and industry through compelling case studies.
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Affiliation(s)
- Aashutosh Girish Boob
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Junyu Chen
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.
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5
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Feng T, Liu J, Zhang X, Fan D, Bai Y. Protein engineering of multi-enzyme virus-like particle nanoreactors for enhanced chiral alcohol synthesis. NANOSCALE ADVANCES 2023; 5:6606-6616. [PMID: 38024302 PMCID: PMC10662152 DOI: 10.1039/d3na00515a] [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: 07/12/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023]
Abstract
In the past decade, virus-like particles (VLPs) that can encapsulate single or multiple enzymes have been studied extensively as typical nanoreactors for biocatalysis in vitro, yet their catalytic efficiencies are usually inadequate for real applications. These biocatalytic nanoreactors should be engineered like their free-enzyme counterparts to improve their catalytic performance for potential applications. Herein we engineer biocatalytic VLPs for the enhanced synthesis of chiral alcohols. Different methods including directed evolution were applied to the entire bacteriophage P22 VLPs (except the coat protein), which encapsulated a carbonyl reductase from Scheffersomyces stipitis (SsCR) and a glucose dehydrogenase from Bacillus megaterium (BmGDH) in their capsids. The best variant, namely M5, showed an enhanced turnover frequency (TOF, min-1) up to 15-fold toward the majority of tested aromatic prochiral ketones, and gave up to 99% enantiomeric excess in the synthesis of chiral alcohol pharmaceutical intermediates. A comparison with the mutations of the free-enzyme counterparts showed that the same amino acid mutations led to different changes in the catalytic efficiencies of free and confined enzymes. Finally, the engineered M5 nanoreactor showed improved efficiency in the scale-up synthesis of chiral alcohols. The conversions of three substrates catalyzed by M5 were all higher than those catalyzed by the wild-type nanoreactor, demonstrating that enzyme-encapsulating VLPs can evolve to enhance their catalytic performance for potential applications.
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Affiliation(s)
- Taotao Feng
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology Shanghai 200237 China
| | - Jiaxu Liu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology Shanghai 200237 China
| | - Xiaoyan Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology Shanghai 200237 China
| | - Daidi Fan
- Shaanxi R&D Centre of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University Xi'an Shaanxi 710069 China
| | - Yunpeng Bai
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology Shanghai 200237 China
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6
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Cheah LC, Liu L, Plan MR, Peng B, Lu Z, Schenk G, Vickers CE, Sainsbury F. Product Profiles of Promiscuous Enzymes Can be Altered by Controlling In Vivo Spatial Organization. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303415. [PMID: 37750486 PMCID: PMC10646250 DOI: 10.1002/advs.202303415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/31/2023] [Indexed: 09/27/2023]
Abstract
Enzyme spatial organization is an evolved mechanism for facilitating multi-step biocatalysis and can play an important role in the regulation of promiscuous enzymes. The latter function suggests that artificial spatial organization can be an untapped avenue for controlling the specificity of bioengineered metabolic pathways. A promiscuous terpene synthase (nerolidol synthase) is co-localized and spatially organized with the preceding enzyme (farnesyl diphosphate synthase) in a heterologous production pathway, via translational protein fusion and/or co-encapsulation in a self-assembling protein cage. Spatial organization enhances nerolidol production by ≈11- to ≈62-fold relative to unorganized enzymes. More interestingly, striking differences in the ratio of end products (nerolidol and linalool) are observed with each spatial organization approach. This demonstrates that artificial spatial organization approaches can be harnessed to modulate the product profiles of promiscuous enzymes in engineered pathways in vivo. This extends the application of spatial organization beyond situations where multiple enzymes compete for a single substrate to cases where there is competition among multiple substrates for a single enzyme.
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Affiliation(s)
- Li Chen Cheah
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Dutton ParkSt LuciaQLD4102Australia
- Present address:
Australian Centre for Disease Preparedness5 Portarlington RdEast GeelongVIC3219Australia
| | - Lian Liu
- Metabolomics Australia (Queensland Node)The University of QueenslandSt LuciaQLD4072Australia
| | - Manuel R. Plan
- Metabolomics Australia (Queensland Node)The University of QueenslandSt LuciaQLD4072Australia
| | - Bingyin Peng
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Dutton ParkSt LuciaQLD4102Australia
- ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneQLD4000Australia
- School of Biological and Environmental ScienceQueensland University of TechnologyBrisbaneQLD4000Australia
| | - Zeyu Lu
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneQLD4000Australia
| | - Gerhard Schenk
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQLD4072Australia
| | - Claudia E. Vickers
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Dutton ParkSt LuciaQLD4102Australia
- ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneQLD4000Australia
- School of Biological and Environmental ScienceQueensland University of TechnologyBrisbaneQLD4000Australia
- Centre for Cell Factories and BiopolymersGriffith Institute for Drug DiscoveryGriffith UniversityNathanQLD4111Australia
| | - Frank Sainsbury
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Dutton ParkSt LuciaQLD4102Australia
- Centre for Cell Factories and BiopolymersGriffith Institute for Drug DiscoveryGriffith UniversityNathanQLD4111Australia
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7
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Wu P, Zhao Y, Zhang X, Fan Y, Zhang S, Zhang W, Huo F. Opportunities and Challenges of Metal-Organic Framework Micro/Nano Reactors for Cascade Reactions. JACS AU 2023; 3:2413-2435. [PMID: 37772189 PMCID: PMC10523373 DOI: 10.1021/jacsau.3c00344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 09/30/2023]
Abstract
Building bridges among different types of catalysts to construct cascades is a highly worthwhile pursuit, such as chemo-, bio-, and chemo-bio cascade reactions. Cascade reactions can improve the reaction efficiency and selectivity while reducing steps of separation and purification, thereby promoting the development of "green chemistry". However, compatibility issues in cascade reactions pose significant constraints on the development of this field, particularly concerning the compatibility of diverse catalyst types, reaction conditions, and reaction rates. Metal-organic framework micro/nano reactors (MOF-MNRs) are porous crystalline materials formed by the self-assembly coordination of metal sites and organic ligands, possessing a periodic network structure. Due to the uniform pore size with the capability of controlling selective transfer of substances as well as protecting active substances and the organic-inorganic parts providing reactive microenvironment, MOF-MNRs have attracted significant attention in cascade reactions in recent years. In this Perspective, we first discuss how to address compatibility issues in cascade reactions using MOF-MNRs, including structural design and synthetic strategies. Then we summarize the research progress on MOF-MNRs in various cascade reactions. Finally, we analyze the challenges facing MOF-MNRs and potential breakthrough directions and opportunities for the future.
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Affiliation(s)
- Peng Wu
- Key
Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced
Materials (IAM), Nanjing Tech University (Nanjing Tech), 30 South Puzhu Road, Nanjing 211816, China
| | - Yanhua Zhao
- Frontiers
Science Center for Flexible Electronics, Xi’an Institute of
Flexible Electronics (IFE), Xi’an Institute of Biomedical Materials
& Engineering, Northwestern Polytechnical
University, 127 West
Youyi Road, Xi’an 710072, China
| | - Xinglong Zhang
- Key
Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced
Materials (IAM), Nanjing Tech University (Nanjing Tech), 30 South Puzhu Road, Nanjing 211816, China
| | - Yun Fan
- Key
Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced
Materials (IAM), Nanjing Tech University (Nanjing Tech), 30 South Puzhu Road, Nanjing 211816, China
| | - Suoying Zhang
- Key
Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced
Materials (IAM), Nanjing Tech University (Nanjing Tech), 30 South Puzhu Road, Nanjing 211816, China
| | - Weina Zhang
- Key
Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced
Materials (IAM), Nanjing Tech University (Nanjing Tech), 30 South Puzhu Road, Nanjing 211816, China
| | - Fengwei Huo
- Key
Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced
Materials (IAM), Nanjing Tech University (Nanjing Tech), 30 South Puzhu Road, Nanjing 211816, China
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8
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Kamra A, Das S, Bhatt P, Solra M, Maity T, Rana S. A transient vesicular glue for amplification and temporal regulation of biocatalytic reaction networks. Chem Sci 2023; 14:9267-9282. [PMID: 37712020 PMCID: PMC10498679 DOI: 10.1039/d3sc00195d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 07/27/2023] [Indexed: 09/16/2023] Open
Abstract
Regulation of enzyme activity and biocatalytic cascades on compartmentalized cellular components is key to the adaptation of cellular processes such as signal transduction and metabolism in response to varying external conditions. Synthetic molecular glues have enabled enzyme inhibition and regulation of protein-protein interactions. So far, all the molecular glue systems based on covalent interactions operated under steady-state conditions. To emulate dynamic biological processes under dissipative conditions, we introduce herein a transient supramolecular glue with a controllable lifetime. The transient system uses multivalent supramolecular interactions between guanidinium group-bearing surfactants and adenosine triphosphate (ATP), resulting in bilayer vesicle structures. Unlike the conventional chemical agents for dissipative assemblies, ATP here plays the dual role of providing a structural component for the assembly as well as presenting active functional groups to "glue" enzymes on the surface. While gluing of the enzymes on the vesicles achieves augmented catalysis, oscillation of ATP concentration allows temporal control of the catalytic activities similar to the dissipative cellular nanoreactors. We further demonstrate temporal upregulation and control of complex biocatalytic reaction networks on the vesicles. Altogether, the temporal activation of biocatalytic cascades on the dissipative vesicular glue presents an adaptable and dynamic system emulating heterogeneous cellular processes, opening up avenues for effective protocell construction and therapeutic interventions.
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Affiliation(s)
- Alisha Kamra
- Materials Research Centre, Indian Institute of Science C.V. Raman Road Bangalore 560012 Karnataka India +9180-22932914
| | - Sourav Das
- Materials Research Centre, Indian Institute of Science C.V. Raman Road Bangalore 560012 Karnataka India +9180-22932914
| | - Preeti Bhatt
- Materials Research Centre, Indian Institute of Science C.V. Raman Road Bangalore 560012 Karnataka India +9180-22932914
| | - Manju Solra
- Materials Research Centre, Indian Institute of Science C.V. Raman Road Bangalore 560012 Karnataka India +9180-22932914
| | - Tanmoy Maity
- Materials Research Centre, Indian Institute of Science C.V. Raman Road Bangalore 560012 Karnataka India +9180-22932914
| | - Subinoy Rana
- Materials Research Centre, Indian Institute of Science C.V. Raman Road Bangalore 560012 Karnataka India +9180-22932914
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9
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Gu Y, Alam S, Oliferenko S. Peroxisomal compartmentalization of amino acid biosynthesis reactions imposes an upper limit on compartment size. Nat Commun 2023; 14:5544. [PMID: 37684233 PMCID: PMC10491753 DOI: 10.1038/s41467-023-41347-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
Cellular metabolism relies on just a few redox cofactors. Selective compartmentalization may prevent competition between metabolic reactions requiring the same cofactor. Is such compartmentalization necessary for optimal cell function? Is there an optimal compartment size? Here we probe these fundamental questions using peroxisomal compartmentalization of the last steps of lysine and histidine biosynthesis in the fission yeast Schizosaccharomyces japonicus. We show that compartmentalization of these NAD+ dependent reactions together with a dedicated NADH/NAD+ recycling enzyme supports optimal growth when an increased demand for anabolic reactions taxes cellular redox balance. In turn, compartmentalization constrains the size of individual organelles, with larger peroxisomes accumulating all the required enzymes but unable to support both biosynthetic reactions at the same time. Our reengineering and physiological experiments indicate that compartmentalized biosynthetic reactions are sensitive to the size of the compartment, likely due to scaling-dependent changes within the system, such as enzyme packing density.
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Affiliation(s)
- Ying Gu
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, UK.
| | - Sara Alam
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, UK
- Medical Research Council London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, UK.
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10
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Wang Q, Chen K, Jiang H, Chen C, Xiong C, Chen M, Xu J, Gao X, Xu S, Zhou H, Wu Y. Cell-inspired design of cascade catalysis system by 3D spatially separated active sites. Nat Commun 2023; 14:5338. [PMID: 37660124 PMCID: PMC10475024 DOI: 10.1038/s41467-023-41002-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 08/10/2023] [Indexed: 09/04/2023] Open
Abstract
Cells possess isolated compartments that spatially confine different enzymes, enabling high-efficiency enzymatic cascade reactions. Herein, we report a cell-inspired design of biomimetic cascade catalysis system by immobilizing Fe single atoms and Au nanoparticles on the inner and outer layers of three-dimensional nanocapsules, respectively. The different metal sites catalyze independently and work synergistically to enable engineered and cascade glucose detection. The biomimetic catalysis system demonstrates ~ 9.8- and 2-fold cascade activity enhancement than conventional mixing and coplanar construction systems, respectively. Furthermore, the biomimetic catalysis system is successfully demonstrated for the colorimetric glucose detection with high catalytic activity and selectivity. Also, the proposed gel-based sensor is integrated with smartphone to enable real-time and visual determination of glucose. More importantly, the gel-based sensor exhibits a high correlation with a commercial glucometer in real samples detection. These findings provide a strategy to design an efficient biomimetic catalysis system for applications in bioassays and nanobiomedicines.
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Affiliation(s)
- Qiuping Wang
- Department of Endocrinology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, 230026, China
| | - Kui Chen
- Key Laboratory of Strongly Coupled Quantum Matter Physics, Chinese Academy of Sciences, School of Physical Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Hui Jiang
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Cai Chen
- Department of Endocrinology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Can Xiong
- Department of Endocrinology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Min Chen
- Department of Endocrinology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Jie Xu
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, 325035, China
| | - Xiaoping Gao
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, 230026, China.
| | - Suowen Xu
- Department of Endocrinology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China.
| | - Huang Zhou
- Department of Endocrinology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China.
| | - Yuen Wu
- Department of Endocrinology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China.
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, 230026, China.
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11
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Huber MC, Schreiber A, Stühn LG, Schiller SM. Programming protein phase-separation employing a modular library of intrinsically disordered precision block copolymer-like proteins creating dynamic cytoplasmatic compartmentalization. Biomaterials 2023; 299:122165. [PMID: 37290157 DOI: 10.1016/j.biomaterials.2023.122165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 05/07/2023] [Accepted: 05/16/2023] [Indexed: 06/10/2023]
Abstract
The control of supramolecular complexes in living systems at the molecular level is an important goal in life-sciences. Spatiotemporal organization of molecular distribution & flow of such complexes are essential physicochemical processes in living cells and important for pharmaceutical processes. Membraneless organelles (MO) found in eukaryotic cells, formed by liquid-liquid phase-separation (LLPS) of intrinsically disordered proteins (IDPs) control and adjust intracellular organization. Artificially designed compartments based on LLPS open up a novel pathway to control chemical flux and partition in vitro and in vivo. We designed a library of chemically precisely defined block copolymer-like proteins based on elastin-like proteins (ELPs) with defined charge distribution and type, as well as polar and hydrophobic block domains. This enables the programmability of physicochemical properties and to control adjustable LLPS in vivo attaining control over intracellular partitioning and flux as role model for in vitro and in vivo applications. Tailor-made ELP-like block copolymer proteins exhibiting IDP-behavior enable LLPS formation in vitro and in vivo allowing the assembly of membrane-based and membraneless superstructures via protein phase-separation in E. coli. Subsequently, we demonstrate the responsiveness of protein phase-separated spaces (PPSSs) to environmental physicochemical triggers and their selective, charge-dependent and switchable interaction with DNA or extrinsic and intrinsic molecules enabling their selective shuttling across semipermeable phase boundaries including (cell)membranes. This paves the road for adjustable artificial PPSS-based storage and reaction spaces and the specific transport across phase boundaries for applications in pharmacy and synthetic biology.
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Affiliation(s)
- Matthias C Huber
- Institut für Pharmazeutische Technologie, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438, Frankfurt, Germany
| | - Andreas Schreiber
- Hahn-Schickard Gesellschaft für angewandte Forschung e. V., Georges-Köhler-Allee 103, D-79110, Freiburg, Germany
| | - Lara G Stühn
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72076, Tübingen, Germany
| | - Stefan M Schiller
- Institut für Pharmazeutische Technologie, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438, Frankfurt, Germany.
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12
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Kramer HM, Cook DE, Seidl MF, Thomma BP. Epigenetic regulation of nuclear processes in fungal plant pathogens. PLoS Pathog 2023; 19:e1011525. [PMID: 37535497 PMCID: PMC10399791 DOI: 10.1371/journal.ppat.1011525] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023] Open
Abstract
Through the association of protein complexes to DNA, the eukaryotic nuclear genome is broadly organized into open euchromatin that is accessible for enzymes acting on DNA and condensed heterochromatin that is inaccessible. Chemical and physical alterations to chromatin may impact its organization and functionality and are therefore important regulators of nuclear processes. Studies in various fungal plant pathogens have uncovered an association between chromatin organization and expression of in planta-induced genes that are important for pathogenicity. This review discusses chromatin-based regulation mechanisms as determined in the fungal plant pathogen Verticillium dahliae and relates the importance of epigenetic transcriptional regulation and other nuclear processes more broadly in fungal plant pathogens.
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Affiliation(s)
- H. Martin Kramer
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
| | - David E. Cook
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America
| | - Michael F. Seidl
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Bart P.H.J. Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
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13
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Tian D, Hao R, Zhang X, Shi H, Wang Y, Liang L, Liu H, Yang H. Multi-compartmental MOF microreactors derived from Pickering double emulsions for chemo-enzymatic cascade catalysis. Nat Commun 2023; 14:3226. [PMID: 37270555 DOI: 10.1038/s41467-023-38949-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/22/2023] [Indexed: 06/05/2023] Open
Abstract
Bioinspired multi-compartment architectures are desired in synthetic biology and metabolic engineering, as credited by their cell-like structures and intrinsic ability of assembling catalytic species for spatiotemporal control over cascade reactions like in living systems. Herein, we describe a general Pickering double emulsion-directed interfacial synthesis method for the fabrication of multicompartmental MOF microreactors. This approach employs multiple liquid-liquid interfaces as a controllable platform for the self-completing growth of dense MOF layers, enabling the microreactor with tailor-made inner architectures and selective permeability. Importantly, simultaneous encapsulation of incompatible functionalities, including hydrophilic enzyme and hydrophobic molecular catalyst, can be realized in a single MOF microreactor for operating chemo-enzymatic cascade reactions. As exemplified by the Grubb' catalyst/CALB lipase driven olefin metathesis/ transesterification cascade reaction and glucose oxidase (GOx)/Fe-porphyrin catalyzed oxidation reaction, the multicompartmental microreactor exhibits 2.24-5.81 folds enhancement in cascade reaction efficiency in comparison to the homogeneous counterparts or physical mixture of individual analogues, due to the restrained mutual inactivation and substrate channelling effects. Our study prompts further design of multicompartment systems and the development of artificial cells capable of complex cellular transformations.
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Affiliation(s)
- Danping Tian
- School of Chemistry and Chemical Engineering, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, China
| | - Ruipeng Hao
- School of Chemistry and Chemical Engineering, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, China
| | - Xiaoming Zhang
- School of Chemistry and Chemical Engineering, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, China.
| | - Hu Shi
- School of Chemistry and Chemical Engineering, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, China
| | - Yuwei Wang
- School of Chemistry and Chemical Engineering, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, China
| | - Linfeng Liang
- Institute of Crystalline Materials, Shanxi University, Taiyuan, 030006, China
| | - Haichao Liu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
| | - Hengquan Yang
- School of Chemistry and Chemical Engineering, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, China.
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14
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Ahn SH, Borden LK, Bentley WE, Raghavan SR. Cell-Like Capsules with "Smart" Compartments. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206693. [PMID: 36895073 DOI: 10.1002/smll.202206693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 02/05/2023] [Indexed: 06/08/2023]
Abstract
Eukaryotic cells have inner compartments (organelles), each with distinct properties and functions. One mimic of this architecture, based on biopolymers, is the multicompartment capsule (MCC). Here, MCCs in which the inner compartments are chemically unique and "smart," i.e., responsive to distinct stimuli in an orthogonal manner are created. Specifically, one compartment alone is induced to degrade when the MCC is contacted with an enzyme while other compartments remain unaffected. Similarly, just one compartment gets degraded upon contact with reactive oxygen species generated from hydrogen peroxide (H2 O2 ). And thirdly, one compartment alone is degraded by an external, physical stimulus, namely, by irradiating the MCC with ultraviolet (UV) light. All these specific responses are achieved without resorting to complicated chemistry to create the compartments: the multivalent cation used to crosslink the biopolymer alginate (Alg) is simply altered. Compartments of Alg crosslinked by Ca2+ are shown to be sensitive to enzymes (alginate lyases) but not to H2 O2 or UV, whereas the reverse is the case with Alg/Fe3+ compartments. These results imply the ability to selectively burst open a compartment in an MCC "on-demand" (i.e., as and when needed) and using biologically relevant stimuli. The results are then extended to a sequential degradation, where compartments in an MCC are degraded one after another, leaving behind an empty MCC lumen. Collectively, this work advances the MCC as a platform that not only emulates key features of cellular architecture, but can also begin to capture rudimentary cell-like behaviors.
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Affiliation(s)
- So Hyun Ahn
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Leah K Borden
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - William E Bentley
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, 20742, USA
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Srinivasa R Raghavan
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, 20742, USA
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
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15
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Turali-Emre ES, Emre AE, Vecchio DA, Kadiyala U, VanEpps JS, Kotov NA. Self-Organization of Iron Sulfide Nanoparticles into Complex Multicompartment Supraparticles. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2211244. [PMID: 36965166 PMCID: PMC10265277 DOI: 10.1002/adma.202211244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/02/2023] [Indexed: 06/09/2023]
Abstract
Self-assembled compartments from nanoscale components are found in all life forms. Their characteristic dimensions are in 50-1000 nm scale, typically assembled from a variety of bioorganic "building blocks". Among the various functions that these mesoscale compartments carry out, protection of the content from the environment is central. Finding synthetic pathways to similarly complex and functional particles from technologically friendly inorganic nanoparticles (NPs) is needed for a multitude of biomedical, biochemical, and biotechnological processes. Here, it is shown that FeS2 NPs stabilized by l-cysteine self-assemble into multicompartment supraparticles (mSPs). The NPs initially produce ≈55 nm concave assemblies that reconfigure into ≈75 nm closed mSPs with ≈340 interconnected compartments with an average size of ≈5 nm. The intercompartmental partitions and mSP surface are formed primarily from FeS2 and Fe2 O3 NPs, respectively. The intermediate formation of cup-like particles enables encapsulation of biological cargo. This capability is demonstrated by loading mSPs with DNA and subsequent transfection of mammalian cells. Also it is found that the temperature stability of the DNA cargo is enhanced compared to the traditional delivery vehicles. These findings demonstrate that biomimetic compartmentalized particles can be used to successfully encapsulate and enhance temperature stability of the nucleic acid cargo for a variety of bioapplications.
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Affiliation(s)
- E. Sumeyra Turali-Emre
- Biomedical Engineering Department, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute University of Michigan; University of Michigan; Ann Arbor, MI, 48109, USA
| | - Ahmet E. Emre
- Biomedical Engineering Department, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute University of Michigan; University of Michigan; Ann Arbor, MI, 48109, USA
| | - Drew A. Vecchio
- Chemical Engineering Department, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute University of Michigan; University of Michigan; Ann Arbor, MI, 48109, USA
| | - Usha Kadiyala
- Department of Emergency Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute University of Michigan; University of Michigan; Ann Arbor, MI, 48109, USA
| | - J. Scott VanEpps
- Department of Emergency Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
- Macromolecular Science and Engineering Department, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute University of Michigan; University of Michigan; Ann Arbor, MI, 48109, USA
| | - Nicholas A. Kotov
- Biomedical Engineering Department, University of Michigan, Ann Arbor, MI, 48109, USA
- Chemical Engineering Department, University of Michigan, Ann Arbor, MI, 48109, USA
- Materials Science and Engineering Department, University of Michigan Ann Arbor, MI, 48109, USA
- Macromolecular Science and Engineering Department, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute University of Michigan; University of Michigan; Ann Arbor, MI, 48109, USA
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16
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Abstract
Encapsulins are a recently discovered class of prokaryotic self-assembling icosahedral protein nanocompartments measuring between 24 and 42 nm in diameter, capable of selectively encapsulating dedicated cargo proteins in vivo. They have been classified into four families based on sequence identity and operon structure, and thousands of encapsulin systems have recently been computationally identified across a wide range of bacterial and archaeal phyla. Cargo encapsulation is mediated by the presence of specific targeting motifs found in all native cargo proteins that interact with the interior surface of the encapsulin shell during self-assembly. Short C-terminal targeting peptides (TPs) are well documented in Family 1 encapsulins, while more recently, larger N-terminal targeting domains (TDs) have been discovered in Family 2. The modular nature of TPs and their facile genetic fusion to non-native cargo proteins of interest has made cargo encapsulation, both in vivo and in vitro, readily exploitable and has therefore resulted in a range of rationally engineered nano-compartmentalization systems. This review summarizes current knowledge on cargo protein encapsulation within encapsulins and highlights select studies that utilize TP fusions to non-native cargo in creative and useful ways.
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Affiliation(s)
- Jesse A Jones
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Robert Benisch
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
| | - Tobias W Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA.
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
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17
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Archer RJ, Hamada S, Shimizu R, Nomura SIM. Scalable Synthesis of Planar Macroscopic Lipid-Based Multi-Compartment Structures. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:4863-4871. [PMID: 36973945 PMCID: PMC10100540 DOI: 10.1021/acs.langmuir.2c02859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/28/2023] [Indexed: 06/18/2023]
Abstract
As life evolved, the path from simple single cell organisms to multicellular enabled increasingly complex functionalities. The spatial separation of reactions at the micron scale achieved by cellular structures allowed diverse and scalable implementation in biomolecular systems. Mimicking such spatially separated domains in a scalable approach could open a route to creating synthetic cell-like structured systems. Here, we report a facile and scalable method to create multicellular-like, multi-compartment (MC) structures. Aqueous droplet-based compartments ranging from 50 to 400 μm were stabilized and connected together by hydrophobic layers composed of phospholipids and an emulsifier. Planar centimeter-scale MC structures were formed by droplet deposition on a water interface. Further, the resulting macroscopic shapes were shown to be achieved by spatially controlled deposition. To demonstrate configurability and potential versatility, MC assemblies of both homogeneous and mixed compartment types were shown. Notably, magnetically heterogeneous systems were achieved by the inclusion of magnetic nanoparticles in defined sections. Such structures demonstrated actuated motion with structurally imparted directionality. These novel and functionalized structures exemplify a route toward future applications including compartmentally assembled "multicellular" molecular robots.
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18
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Hu L, Wang Y, Wang L, Xiao S, Zheng Y, Yin G, Du G, Chen J, Kang Z. Construction of Osmotic Pressure Responsive Vacuole-like Bacterial Organelles with Capsular Polysaccharides as Building Blocks. ACS Synth Biol 2023; 12:750-760. [PMID: 36872621 DOI: 10.1021/acssynbio.2c00546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Many artificial organelles or subcellular compartments have been developed to tune gene expression, regulate metabolic pathways, or endow new cell functions. Most of these organelles or compartments were built using proteins or nucleic acids as building blocks. In this study, we demonstrated that capsular polysaccharide (CPS) retained inside bacteria cytosol assembled into mechanically stable CPS compartments. The CPS compartments were able to accommodate and release protein molecules but not lipids or nucleic acids. Intriguingly, we found that the CPS compartment size responds to osmotic stress and this compartment improves cell survival under high osmotic pressures, which was similar to the vacuole functionalities. By fine-tuning the synthesis and degradation of CPS with osmotic stress-responsive promoters, we achieved dynamic regulation of the size of CPS compartments and the host cells in response to external osmotic stress. Our results shed new light on developing prokaryotic artificial organelles with carbohydrate macromolecules.
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Affiliation(s)
- Litao Hu
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yang Wang
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Lingling Wang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Sen Xiao
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yilin Zheng
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guobin Yin
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jian Chen
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhen Kang
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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19
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Huang J, Gambietz S, Saccà B. Self-Assembled Artificial DNA Nanocompartments and Their Bioapplications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2202253. [PMID: 35775957 DOI: 10.1002/smll.202202253] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Compartmentalization is the strategy evolved by nature to control reactions in space and time. The ability to emulate this strategy through synthetic compartmentalization systems has rapidly evolved in the past years, accompanied by an increasing understanding of the effects of spatial confinement on the thermodynamic and kinetic properties of the guest molecules. DNA nanotechnology has played a pivotal role in this scientific endeavor and is still one of the most promising approaches for the construction of nanocompartments with programmable structural features and nanometer-scaled addressability. In this review, the design approaches, bioapplications, and theoretical frameworks of self-assembled DNA nanocompartments are surveyed. From DNA polyhedral cages to virus-like capsules, the construction principles of such intriguing architectures are illustrated. Various applications of DNA nanocompartments, including their use for programmable enzyme scaffolding, single-molecule studies, biosensing, and as artificial nanofactories, ending with an ample description of DNA nanocages for biomedical purposes, are then reported. Finally, the theoretical hypotheses that make DNA nanocompartments, and nanosystems in general, a topic of great interest in modern science, are described and the progresses that have been done until now in the comprehension of the peculiar phenomena that occur within nanosized environments are summarized.
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Affiliation(s)
- Jing Huang
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
| | - Sabrina Gambietz
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
| | - Barbara Saccà
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
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20
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Li G, Liu H, Yi J, Pu F, Ren J, Qu X. Integrating Incompatible Nanozyme-Catalyzed Reactions for Diabetic Wound Healing. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206707. [PMID: 36541749 DOI: 10.1002/smll.202206707] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/04/2022] [Indexed: 06/17/2023]
Abstract
Multi-nanozymes are widely applied in disease treatment, biosensing, and other fields. However, most current multi-nanozyme systems exhibit only moderate activity since reaction microenvironments of different nanozyme are often distinct or even incompatible. Conventional assemble strategies are inapplicable for designing multi-nanozymes consisting of incompatible nanozymes. Herein, a versatile fiber-based compartmentalization strategy is developed to construct multi-nanozyme system capable of simultaneously performing incompatible reactions. In this system, the incompatible nanozymes are spatially distributed in distinct compartmentalized fibers, where different microenvironments can be tailored by controlling the doping reagent, endowing each nanozymes with the preferential microenvironments to exhibit their highest activity. As a proof of concept, pH-incompatible peroxidase-like and catalase-like catalytic reactions are tested to verify the feasibility of this strategy. By doping with benzoic acid in the desired location, the two pH-incompatible nanozymes can work simultaneously without interference. Further, it is demonstrated that the oxygen supply and antimicrobial power of the integrated platform can be applied for accelerating diabetic wound healing. It is hoped that this work provides a way to integrate incompatible nanozyme and broadens the application potential of multi-nanozymes.
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Affiliation(s)
- Guangming Li
- State Key Laboratory of Rare Earth Resources Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
| | - Hao Liu
- State Key Laboratory of Rare Earth Resources Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Jiadai Yi
- State Key Laboratory of Rare Earth Resources Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Fang Pu
- State Key Laboratory of Rare Earth Resources Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Jinsong Ren
- State Key Laboratory of Rare Earth Resources Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Xiaogang Qu
- State Key Laboratory of Rare Earth Resources Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
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21
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Ferreras S, Singh NP, Le Borgne R, Bun P, Binz T, Parton RG, Verbavatz JM, Vannier C, Galli T. A synthetic organelle approach to probe SNARE-mediated membrane fusion in a bacterial host. J Biol Chem 2023; 299:102974. [PMID: 36738791 PMCID: PMC10011478 DOI: 10.1016/j.jbc.2023.102974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
In vivo and in vitro assays, particularly reconstitution using artificial membranes, have established the role of synaptic soluble N-Ethylmaleimide-sensitive attachment protein receptors (SNAREs) VAMP2, Syntaxin-1A, and SNAP-25 in membrane fusion. However, using artificial membranes requires challenging protein purifications that could be avoided in a cell-based assay. Here, we developed a synthetic biological approach based on the generation of membrane cisternae by the integral membrane protein Caveolin in Escherichia coli and coexpression of SNAREs. Syntaxin-1A/SNAP-25/VAMP-2 complexes were formed and regulated by SNARE partner protein Munc-18a in the presence of Caveolin. Additionally, Syntaxin-1A/SNAP-25/VAMP-2 synthesis provoked increased length of E. coli only in the presence of Caveolin. We found that cell elongation required SNAP-25 and was inhibited by tetanus neurotoxin. This elongation was not a result of cell division arrest. Furthermore, electron and super-resolution microscopies showed that synaptic SNAREs and Caveolin coexpression led to the partial loss of the cisternae, suggesting their fusion with the plasma membrane. In summary, we propose that this assay reconstitutes membrane fusion in a simple organism with an easy-to-observe phenotype and is amenable to structure-function studies of SNAREs.
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Affiliation(s)
- Soledad Ferreras
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM, Membrane Traffic in Healthy & Diseased Brain, Paris, France
| | - Neha Pratap Singh
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM, Membrane Traffic in Healthy & Diseased Brain, Paris, France
| | - Remi Le Borgne
- Université Paris Cité, CNRS, UMR7592, Institut Jacques Monod, Paris, France
| | - Philippe Bun
- Université Paris Cité, NeurImag, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Paris, France
| | - Thomas Binz
- Institute of Cell Biochemistry, Hannover Medical School, Hannover, Germany
| | - Robert G Parton
- The University of Queensland, Institute for Molecular Bioscience and Centre for Microscopy and Microanalysis, Qld, Brisbane, Australia
| | | | - Christian Vannier
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM, Membrane Traffic in Healthy & Diseased Brain, Paris, France.
| | - Thierry Galli
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM, Membrane Traffic in Healthy & Diseased Brain, Paris, France; GHU Paris psychiatrie neurosciences, Paris, France.
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22
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Liu Y, Wang X, Wan Z, Ngai T, Tse YLS. Capturing coacervate formation and protein partition by molecular dynamics simulation. Chem Sci 2023; 14:1168-1175. [PMID: 36756326 PMCID: PMC9891350 DOI: 10.1039/d2sc01164f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 12/22/2022] [Indexed: 12/25/2022] Open
Abstract
Biomolecules localize and function in microenvironments where their local concentration, spatial organization, and biochemical reactivity are regulated. To compartmentalize and control the local properties of the native microenvironment, cellular mimics and artificial bioreactors have been developed to study the properties of membraneless organelles or mimic the bio-environment for life origin. Here, we carried out molecular dynamics simulation with the Martini 3.0 model to reproduce the experimental salt concentration and pH dependency of different complex coacervates. We showed that coacervates inside vesicles are able to change their shape. In addition, we used these coacervate systems to explore the partitioning of the ubiquitous cytoskeletal protein actin and found that actin spontaneously partitions to all the coacervate peripheries. Therefore, we believe that our study can provide a better understanding of the versatile coacervate platform, where biomolecules partition and gather to fulfill their biological duties.
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Affiliation(s)
- Yang Liu
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University Chengdu 610065 China.,Department of Chemistry, The Chinese University of Hong Kong Sha Tin Hong Kong China
| | - Xinyan Wang
- Department of Chemistry, The Chinese University of Hong Kong Sha Tin Hong Kong China
| | - Zhili Wan
- School of Food Science and Engineering, South China University of TechnologyGuangzhouChina
| | - To Ngai
- Department of Chemistry, The Chinese University of Hong Kong Sha Tin Hong Kong China
| | - Ying-Lung Steve Tse
- Department of Chemistry, The Chinese University of Hong Kong Sha Tin Hong Kong China
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23
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Sousa A, Phung AN, Škalko-Basnet N, Obuobi S. Smart delivery systems for microbial biofilm therapy: Dissecting design, drug release and toxicological features. J Control Release 2023; 354:394-416. [PMID: 36638844 DOI: 10.1016/j.jconrel.2023.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/14/2022] [Accepted: 01/02/2023] [Indexed: 01/15/2023]
Abstract
Bacterial biofilms are highly protected surface attached communities of bacteria that typically cause chronic infections. To address their recalcitrance to antibiotics and minimise side effects of current therapies, smart drug carriers are being explored as promising platforms for antimicrobials. Herein, we briefly summarize recent efforts and considerations that have been applied in the design of these smart carriers. We guide readers on a journey on how they can leverage the inherent biofilm microenvironment, external stimuli, or combine both types of stimuli in a predictable manner. The specific carrier features that are responsible for their 'on-demand' properties are detailed and their impact on antibiofilm property are further discussed. Moreover, an analysis on the impact of such features on drug release profiles is provided. Since nanotechnology represents a significant slice of the drug delivery pie, some insights on the potential toxicity are also depicted. We hope that this review inspires researchers to use their knowledge and creativity to design responsive systems that can eradicate biofilm infections.
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Affiliation(s)
- A Sousa
- Drug Transport and Delivery Research Group, Department of Pharmacy, UIT The Arctic University of Norway, Tromsø, Norway
| | - A Ngoc Phung
- Drug Transport and Delivery Research Group, Department of Pharmacy, UIT The Arctic University of Norway, Tromsø, Norway
| | - N Škalko-Basnet
- Drug Transport and Delivery Research Group, Department of Pharmacy, UIT The Arctic University of Norway, Tromsø, Norway
| | - S Obuobi
- Drug Transport and Delivery Research Group, Department of Pharmacy, UIT The Arctic University of Norway, Tromsø, Norway.
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24
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Konishi H, Nakata E, Komatsubara F, Morii T. Controlled Assembly of Fluorophores inside a Nanoliposome. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020911. [PMID: 36677968 PMCID: PMC9864194 DOI: 10.3390/molecules28020911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/13/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023]
Abstract
Cellular compartmentalization plays an essential role in organizing the complex and multiple biochemical reactions in the cell. An artificial compartment would provide powerful strategies to develop new biochemical tools for material production and diagnosis, but it is still a great challenge to synthesize the compartments that encapsulate materials of interest while controlling their accurate locations, numbers, and stoichiometry. In this study, we evaluated chemical characteristics of a liposome-encapsulated compartment, which has great potential to locate various materials of interest with precise control of their locations and numbers in the compartment. A nanoliposome was constructed inside a ring-shaped DNA origami skeleton according to the method of Yang et al., and further equipped with a double-stranded DNA platform to assemble molecules of interest in the nanoliposome. Upon formation of the nanoliposome, a pH-sensitive fluorophore on the bridged platform showed little or no response to the pH change of the outer buffer, ensuring that the molecules assembled on the platform are effectively shielded from the outer environment. The ring-shaped DNA skeleton equipped with a double-stranded DNA platform allows spatial assembly of several functional molecules inside the nanoliposome to isolate them from the outer environment.
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25
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Zhao Y, Gao S, Song D, Ye Z, Xu R, Luo Y, Xu Q. Lipidoid Artificial Compartments for Bidirectional Regulation of Enzyme Activity through Nanomechanical Action. J Am Chem Soc 2023; 145:551-559. [PMID: 36537880 DOI: 10.1021/jacs.2c11004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Photoresponsive inhibitor and noninhibitor systems have been developed to achieve on-demand enzyme activity control. However, inhibitors are only effective for a specific and narrow range of enzymes. Noninhibitor systems usually require mutation and modification of the enzymes, leading to irreversible loss of enzymatic activities. Inspired by biological membranes, we herein report a lipidoid-based artificial compartment composed of azobenzene (Azo) lipidoids and helper lipids, which can bidirectionally regulate the activity of the encapsulated enzymes by light. In this system, the reversible photoisomerization of Azo lipidoids triggered by UV/vis light creates a continuous rotation-inversion movement, thereby enhancing the permeability of the compartment membrane and allowing substrates to pass through. Moreover, the membrane can revert to its impermeable state when light is removed. Thus, enzyme activity can be switched on and off when encapsulating enzymes in the compartments. Importantly, since neither mutation nor modification is required, negligible loss of activity is observed for the encapsulated enzymes after repeated activation and inhibition. Furthermore, this approach provides a generic strategy for controlling multiple enzymes by forgoing the use of inhibitors and may broaden the applications of enzymes in biological mechanism research and precision medicine.
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Affiliation(s)
- Yu Zhao
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Shuliang Gao
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Donghui Song
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Zhongfeng Ye
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Ruijie Xu
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Ying Luo
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Qiaobing Xu
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
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26
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Nakata E, Dinh H, Lin P, Morii T. Enzyme Cascade Reactions on DNA Origami Scaffold. Methods Mol Biol 2023; 2639:275-299. [PMID: 37166723 DOI: 10.1007/978-1-0716-3028-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The protocols for constructing, characterizing, and analyzing enzyme cascade reaction systems on the DNA scaffold are described. Two-step and three-step enzyme cascade reactions were adapted from the xylose metabolic pathway as the example of natural metabolic pathway and were assembled on the DNA scaffold by using the DNA binding adaptors.
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Affiliation(s)
- Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Peng Lin
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan.
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27
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Zhang X, Zeng R, Zhang T, Lv C, Zang J, Zhao G. Spatiotemporal control over 3D protein nanocage superlattices for the hierarchical encapsulation and release of different cargo molecules. J Mater Chem B 2022; 10:9968-9973. [PMID: 36472186 DOI: 10.1039/d2tb01961b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Taking inspiration from Nature, we have constructed a two-compartment system based on 3D ferritin nanocage superlattices, the self-assembly behavior of which can be spatiotemporally controlled using two designed switches. One pH switch regulates the assembly of the ferritin subunit into its shell-like structure, whereas the other metal switch is responsible for assembly of the 3D superlattices from ferritin nanocages as building blocks. Consequently, this system holds great promise for the hierarchical encapsulation and release of two different cargo molecules.
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Affiliation(s)
- Xiaorong Zhang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
| | - Ruiqi Zeng
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
| | - Tuo Zhang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
| | - Chenyan Lv
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
| | - Jiachen Zang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
| | - Guanghua Zhao
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
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28
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Ahn SH, Karlsson AJ, Bentley WE, Raghavan SR. Capsules with bacteria and fungi in distinct compartments: A platform for studying microbes from different kingdoms and their cross-communication. PLoS One 2022; 17:e0277132. [DOI: 10.1371/journal.pone.0277132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 10/21/2022] [Indexed: 11/13/2022] Open
Abstract
Recently, we have created ‘artificial cells’ with an architecture mimicking that of typical eukaryotic cells. Our design uses common biopolymers like alginate and chitosan to create multi-compartment capsules (MCCs) via oil-free microfluidics. MCCs (~ 500 μm in diameter) can be engineered with multiple inner compartments, each with a distinct payload. This mimics the distinct organelles in eukaryotic cells, each of which has unique properties. In this study, we encapsulate microbial cells from two distinct kingdoms — Pseudomonas aeruginosa (bacteria) and Candida albicans (fungi) — in the inner compartments of MCCs. The two microbes are commonly found in biofilms at sites of infection in humans. We first demonstrate that the MCC can serve as a simple platform to observe the comparative growth of the cells in real time. Unlike typical co-culture in solution or on agar plates, the cells can grow in their own compartments without direct physical contact. Moreover, the hydrogel matrix in the compartments mimics the three-dimensional (3-D) environment that cells naturally encounter during their growth. Small molecules added to the solution are shown to permeate through the capsule walls and affect cell growth: for example, cationic surfactants inhibit the fungi but not the bacteria. Conversely, low pH and kanamycin inhibit the bacteria but not the fungi. Also, when the bacteria are present in adjacent compartments, the fungal cells mostly stay in a yeast morphology, meaning as spheroidal cells. In contrast, in the absence of the bacteria, the fungi transition into hyphae, i.e., long multicellular filaments. The inhibition of this morphological switch in fungal cells is shown to be induced by signaling molecules (specifically, the quorum sensing autoinducer-1 or AI-1) secreted by the bacteria. Thus, the MCC platform can also be used to detect cross-kingdom signaling between the compartmentalized microbes.
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29
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Zhang J, Shin J, Tague N, Lin H, Zhang M, Ge X, Wong W, Dunlop MJ, Cheng J. Visualization of a Limonene Synthesis Metabolon Inside Living Bacteria by Hyperspectral SRS Microscopy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203887. [PMID: 36169112 PMCID: PMC9661820 DOI: 10.1002/advs.202203887] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/21/2022] [Indexed: 06/16/2023]
Abstract
Monitoring biosynthesis activity at single-cell level is key to metabolic engineering but is still difficult to achieve in a label-free manner. Using hyperspectral stimulated Raman scattering imaging in the 670-900 cm-1 region, localized limonene synthesis are visualized inside engineered Escherichia coli. The colocalization of limonene and GFP-fused limonene synthase is confirmed by co-registered stimulated Raman scattering and two-photon fluorescence images. The finding suggests a limonene synthesis metabolon with a polar distribution inside the cells. This finding expands the knowledge of de novo limonene biosynthesis in engineered bacteria and highlights the potential of SRS chemical imaging in metabolic engineering research.
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Affiliation(s)
- Jing Zhang
- Department of Biomedical EngineeringBoston UniversityBostonMA02215USA
- Photonics CenterBoston UniversityBostonMA02215USA
| | - Jonghyeon Shin
- Department of Biomedical EngineeringBoston UniversityBostonMA02215USA
| | - Nathan Tague
- Department of Biomedical EngineeringBoston UniversityBostonMA02215USA
- Biological Design CenterBoston UniversityBostonMA02215USA
| | - Haonan Lin
- Department of Biomedical EngineeringBoston UniversityBostonMA02215USA
- Photonics CenterBoston UniversityBostonMA02215USA
| | - Meng Zhang
- Photonics CenterBoston UniversityBostonMA02215USA
- Department of Electrical and Computer EngineeringBoston UniversityBostonMA02215USA
| | - Xiaowei Ge
- Photonics CenterBoston UniversityBostonMA02215USA
- Department of Electrical and Computer EngineeringBoston UniversityBostonMA02215USA
| | - Wilson Wong
- Department of Biomedical EngineeringBoston UniversityBostonMA02215USA
- Biological Design CenterBoston UniversityBostonMA02215USA
| | - Mary J. Dunlop
- Department of Biomedical EngineeringBoston UniversityBostonMA02215USA
- Biological Design CenterBoston UniversityBostonMA02215USA
| | - Ji‐Xin Cheng
- Department of Biomedical EngineeringBoston UniversityBostonMA02215USA
- Photonics CenterBoston UniversityBostonMA02215USA
- Department of Electrical and Computer EngineeringBoston UniversityBostonMA02215USA
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30
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Liu CL, Dong HG, Xue K, Sun L, Yang Y, Liu X, Li Y, Bai Z, Tan TW. Metabolic Engineering Mevalonate Pathway Mediated by RNA Scaffolds for Mevalonate and Isoprene Production in Escherichia coli. ACS Synth Biol 2022; 11:3305-3317. [PMID: 36198145 DOI: 10.1021/acssynbio.2c00226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Co-localizing biochemical processes is a great strategy when expressing the heterologous metabolic pathway for product biosynthesis. The RNA scaffold is a flexible and efficient synthetic compartmentalization method to co-localize the enzymes involved in the metabolic pathway by binding to the specific RNA, binding domains fused with the engineered enzymes. Herein, we designed two artificial RNA scaffold structures─0D RNA scaffolds and 2D RNA scaffolds─using the reported aptamers PP7 and BIV-Tat and the corresponding RNA-binding domains (RBDs). We verified the interaction of the RBD and RNA aptamer in vitro and in vivo. Then, we determined the efficiencies of these RNA scaffolds by co-localizing fluorescent proteins. We employed the RNA scaffolds combined with the enzyme fusion strategies to increase the metabolic flux involved in the enzymes of the mevalonate pathway for mevalonate and isoprene production. Compared with the no RNA scaffold strain, the mevalonate levels of the 0D RNA scaffolds and 2D RNA scaffolds increased by 84.1% (3.13 ± 0.03 g/L) and 76.5% (3.00 ± 0.09 g/L), respectively. We applied the 0D RNA scaffolds for increasing the isoprene production by localizing the enzymes involved in a heterologous multi-enzyme pathway. When applying the RNA scaffolds for co-localizing the enzymes mvaE and mvaS, the isoprene production reached to 609.3 ± 57.9 mg/L, increasing by 142% compared with the no RNA scaffold strain. Our results indicate that the RNA scaffold is a powerful tool for improving the efficiencies of the reaction process in the metabolic pathway.
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Affiliation(s)
- Chun-Li Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Hong-Gang Dong
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Kai Xue
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Li Sun
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Yankun Yang
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Xiuxia Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Ye Li
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Zhonghu Bai
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Tian-Wei Tan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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31
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Reardon TJ, Na B, Parquette JR. Dissipative self-assembly of a proline catalyst for temporal regulation of the aldol reaction. NANOSCALE 2022; 14:14711-14716. [PMID: 36169284 DOI: 10.1039/d2nr03991e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The spatiotemporal regulation of chemical reactivity in biological systems permits a network of metabolic reactions to take place within the same cellular environment. The exquisite control of reactivity is often mediated by out-of-equilibrium structures that remain functional only as long as fuel is present to maintain the higher energy, active state. An important goal in supramolecular chemistry aims to develop functional, energy dissipating systems that approach the sophistication of biological machinery. The challenge is to create strategies that couple the energy consumption needed to promote a molecule to a higher energy, assembled state to a functional property such as catalytic activity. In this work, we demonstrated that the assembly of a spiropyran (SP) dipeptide (1) transiently promoted the proline-catalyzed aldol reaction in water when visible light was present as fuel. The transient catalytic activity emerged from 1 under light illumination due to the photoisomerization of the monomeric, O-protonated (1-MCH+) merocyanine form to the spiropyran (1-SP) state, which rapidly assembled into nanosheets capable of catalyzing the aldol reaction in water. When the light source was removed, thermal isomerization to the more stable MCH+ form caused the nanosheets to dissociate into a catalytically inactive, monomeric state. Under these conditions, the aldol reaction could be repeatedly activated and deactivated by switching the light source on and off.
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Affiliation(s)
- Thomas J Reardon
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W. 18th Ave. Columbus, Ohio 43210, USA.
| | - Baichuan Na
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W. 18th Ave. Columbus, Ohio 43210, USA.
| | - Jon R Parquette
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W. 18th Ave. Columbus, Ohio 43210, USA.
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32
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Lin P, Yang H, Nakata E, Morii T. Mechanistic Aspects for the Modulation of Enzyme Reactions on the DNA Scaffold. Molecules 2022; 27:molecules27196309. [PMID: 36234845 PMCID: PMC9572797 DOI: 10.3390/molecules27196309] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 12/03/2022] Open
Abstract
Cells have developed intelligent systems to implement the complex and efficient enzyme cascade reactions via the strategies of organelles, bacterial microcompartments and enzyme complexes. The scaffolds such as the membrane or protein in the cell are believed to assist the co-localization of enzymes and enhance the enzymatic reactions. Inspired by nature, enzymes have been located on a wide variety of carriers, among which DNA scaffolds attract great interest for their programmability and addressability. Integrating these properties with the versatile DNA–protein conjugation methods enables the spatial arrangement of enzymes on the DNA scaffold with precise control over the interenzyme distance and enzyme stoichiometry. In this review, we survey the reactions of a single type of enzyme on the DNA scaffold and discuss the proposed mechanisms for the catalytic enhancement of DNA-scaffolded enzymes. We also review the current progress of enzyme cascade reactions on the DNA scaffold and discuss the factors enhancing the enzyme cascade reaction efficiency. This review highlights the mechanistic aspects for the modulation of enzymatic reactions on the DNA scaffold.
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33
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Ye DY, Noh MH, Moon JH, Milito A, Kim M, Lee JW, Yang JS, Jung GY. Kinetic compartmentalization by unnatural reaction for itaconate production. Nat Commun 2022; 13:5353. [PMID: 36097012 PMCID: PMC9468356 DOI: 10.1038/s41467-022-33033-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 08/29/2022] [Indexed: 11/09/2022] Open
Abstract
Physical compartmentalization of metabolism using membranous organelles in eukaryotes is helpful for chemical biosynthesis to ensure the availability of substrates from competitive metabolic reactions. Bacterial hosts lack such a membranous system, which is one of the major limitations for efficient metabolic engineering. Here, we employ kinetic compartmentalization with the introduction of an unnatural enzymatic reaction by an engineered enzyme as an alternative strategy to enable substrate availability from competitive reactions through kinetic isolation of metabolic pathways. As a proof of concept, we kinetically isolate the itaconate synthetic pathway from the tricarboxylic acid cycle in Escherichia coli, which is natively separated by mitochondrial membranes in Aspergillus terreus. Specifically, 2-methylcitrate dehydratase is engineered to alternatively catalyze citrate and kinetically secure cis-aconitate for efficient production using a high-throughput screening system. Itaconate production can be significantly improved with kinetic compartmentalization and its strategy has the potential to be widely applicable.
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Affiliation(s)
- Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Myung Hyun Noh
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Jo Hyun Moon
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Alfonsina Milito
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Minsun Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Jeong Wook Lee
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea.,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Jae-Seong Yang
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain.
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea. .,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea.
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34
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Zangiabadi M, Zhao Y. Controlling enzyme reactions by supramolecular protection and deprotection of oligosaccharide substrates. Chem Commun (Camb) 2022; 58:9770-9773. [PMID: 35968858 DOI: 10.1039/d2cc03239b] [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
Protection/deprotection is a powerful strategy in the total synthesis of complex organic molecules but similar tools are nearly absent in enzymatic reactions. We here report supramolecular protective receptors that outcompete an enzyme in the binding of oligosaccharides. The strong binding inhibits the enzymatic reaction and addition of an even stronger ligand for the receptor releases the substrate. These receptors could be used to control products from the same substrate/enzyme mixture and regulate enzymatic reactions reversibly.
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Affiliation(s)
- Milad Zangiabadi
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, USA.
| | - Yan Zhao
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, USA.
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35
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Zhang Q, Liu J, Wu Y. Enzyme Cascade Reaction Propelled Multicompartmental Colloidal Motors. Chem Asian J 2022; 17:e202200560. [PMID: 35761116 DOI: 10.1002/asia.202200560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/26/2022] [Indexed: 11/09/2022]
Abstract
Compartmentalization is a crucial natural methodology to enable multiple biocatalytic transformations to proceed efficiently. Herein, we report a biocompatible multicompartmental colloidal motor that can achieve autonomous movement in the biological environment through two-enzyme cascade reactions of immobilized enzymes. The colloidal motors with the heterogeneous multicompartment structure were prepared in one step by microfluidic technology, and the compartmentalized encapsulation of glucose oxidase (GOD) and catalase (CAT) was realized. The fabricated colloidal motor was size controllable by tuning the flow rates of the microfluidic system, and its autonomous movement can be triggered by good responsiveness to the alkaline environment. In glucose medium of pH 7.5, the pH-responsive alginate cores of the colloidal motor swell to facilitate fuel penetration and enzyme-catalyzed reactions. The enzyme cascade between GOD and CAT immobilized in the colloidal motor chamber results in the self-propulsion of the colloid motor in glucose medium. The compartmentalized encapsulation of immobilized enzyme improves the stability of the enzyme and enables multicompartmental colloidal motors to self-propel in an alkaline intestinal environment through an enzyme cascade reaction. These features indicate that such multicompartmental colloidal motors actuated by enzyme cascade reaction in biocompatible fuel have great potential for co-encapsulation and autonomous movement in different applications.
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Affiliation(s)
- Qihan Zhang
- Harbin Institute of Technology, School of Medicine and Health, CHINA
| | - Jun Liu
- Harbin Institute of Technology, School of Medicine and Health, CHINA
| | - Yingjie Wu
- Harbin Institute of Technology, School of Medicine and Health, No. 92 XiDaZhi Street, 150001, Harbin, CHINA
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36
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Yang M, Wenner N, Dykes GF, Li Y, Zhu X, Sun Y, Huang F, Hinton JCD, Liu LN. Biogenesis of a bacterial metabolosome for propanediol utilization. Nat Commun 2022; 13:2920. [PMID: 35614058 PMCID: PMC9132943 DOI: 10.1038/s41467-022-30608-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 04/22/2022] [Indexed: 12/24/2022] Open
Abstract
Bacterial metabolosomes are a family of protein organelles in bacteria. Elucidating how thousands of proteins self-assemble to form functional metabolosomes is essential for understanding their significance in cellular metabolism and pathogenesis. Here we investigate the de novo biogenesis of propanediol-utilization (Pdu) metabolosomes and characterize the roles of the key constituents in generation and intracellular positioning of functional metabolosomes. Our results demonstrate that the Pdu metabolosome undertakes both "Shell first" and "Cargo first" assembly pathways, unlike the β-carboxysome structural analog which only involves the "Cargo first" strategy. Shell and cargo assemblies occur independently at the cell poles. The internal cargo core is formed through the ordered assembly of multiple enzyme complexes, and exhibits liquid-like properties within the metabolosome architecture. Our findings provide mechanistic insight into the molecular principles driving bacterial metabolosome assembly and expand our understanding of liquid-like organelle biogenesis.
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Affiliation(s)
- Mengru Yang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Nicolas Wenner
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Gregory F Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Yan Li
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Xiaojun Zhu
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Yaqi Sun
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Fang Huang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Jay C D Hinton
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom.
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China.
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37
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Heuberger L, Korpidou M, Eggenberger OM, Kyropoulou M, Palivan CG. Current Perspectives on Synthetic Compartments for Biomedical Applications. Int J Mol Sci 2022; 23:5718. [PMID: 35628527 PMCID: PMC9145047 DOI: 10.3390/ijms23105718] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 12/04/2022] Open
Abstract
Nano- and micrometer-sized compartments composed of synthetic polymers are designed to mimic spatial and temporal divisions found in nature. Self-assembly of polymers into compartments such as polymersomes, giant unilamellar vesicles (GUVs), layer-by-layer (LbL) capsules, capsosomes, or polyion complex vesicles (PICsomes) allows for the separation of defined environments from the exterior. These compartments can be further engineered through the incorporation of (bio)molecules within the lumen or into the membrane, while the membrane can be decorated with functional moieties to produce catalytic compartments with defined structures and functions. Nanometer-sized compartments are used for imaging, theranostic, and therapeutic applications as a more mechanically stable alternative to liposomes, and through the encapsulation of catalytic molecules, i.e., enzymes, catalytic compartments can localize and act in vivo. On the micrometer scale, such biohybrid systems are used to encapsulate model proteins and form multicompartmentalized structures through the combination of multiple compartments, reaching closer to the creation of artificial organelles and cells. Significant progress in therapeutic applications and modeling strategies has been achieved through both the creation of polymers with tailored properties and functionalizations and novel techniques for their assembly.
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Affiliation(s)
- Lukas Heuberger
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, 4058 Basel, Switzerland; (L.H.); (M.K.); (O.M.E.); (M.K.)
| | - Maria Korpidou
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, 4058 Basel, Switzerland; (L.H.); (M.K.); (O.M.E.); (M.K.)
| | - Olivia M. Eggenberger
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, 4058 Basel, Switzerland; (L.H.); (M.K.); (O.M.E.); (M.K.)
| | - Myrto Kyropoulou
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, 4058 Basel, Switzerland; (L.H.); (M.K.); (O.M.E.); (M.K.)
- NCCR-Molecular Systems Engineering, Mattenstrasse 24a, BPR 1095, 4058 Basel, Switzerland
| | - Cornelia G. Palivan
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, 4058 Basel, Switzerland; (L.H.); (M.K.); (O.M.E.); (M.K.)
- NCCR-Molecular Systems Engineering, Mattenstrasse 24a, BPR 1095, 4058 Basel, Switzerland
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38
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Dhasaiyan P, Ghosh T, Lee HG, Lee Y, Hwang I, Mukhopadhyay RD, Park KM, Shin S, Kang IS, Kim K. Cascade reaction networks within audible sound induced transient domains in a solution. Nat Commun 2022; 13:2372. [PMID: 35501325 PMCID: PMC9061750 DOI: 10.1038/s41467-022-30124-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 04/07/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractSpatiotemporal control of chemical cascade reactions within compartmentalized domains is one of the difficult challenges to achieve. To implement such control, scientists have been working on the development of various artificial compartmentalized systems such as liposomes, vesicles, polymersomes, etc. Although a considerable amount of progress has been made in this direction, one still needs to develop alternative strategies for controlling cascade reaction networks within spatiotemporally controlled domains in a solution, which remains a non-trivial issue. Herein, we present the utilization of audible sound induced liquid vibrations for the generation of transient domains in an aqueous medium, which can be used for the control of cascade chemical reactions in a spatiotemporal fashion. This approach gives us access to highly reproducible spatiotemporal chemical gradients and patterns, in situ growth and aggregation of gold nanoparticles at predetermined locations or domains formed in a solution. Our strategy also gives us access to nanoparticle patterned hydrogels and their applications for region specific cell growth.
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39
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Wise L, Marecos S, Randolph K, Hassan M, Nshimyumukiza E, Strouse J, Salimijazi F, Barstow B. Thermodynamic Constraints on Electromicrobial Protein Production. Front Bioeng Biotechnol 2022; 10:820384. [PMID: 35265598 PMCID: PMC8899463 DOI: 10.3389/fbioe.2022.820384] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/14/2022] [Indexed: 02/03/2023] Open
Abstract
Global consumption of protein is projected to double by the middle of the 21st century. However, protein production is one of the most energy intensive and environmentally damaging parts of the food supply system today. Electromicrobial production technologies that combine renewable electricity and CO2-fixing microbial metabolism could dramatically increase the energy efficiency of commodity chemical production. Here we present a molecular-scale model that sets an upper limit on the performance of any organism performing electromicrobial protein production. We show that engineered microbes that fix CO2 and N2 using reducing equivalents produced by H2-oxidation or extracellular electron uptake could produce amino acids with energy inputs as low as 64 MJ kg−1, approximately one order of magnitude higher than any previous estimate of the efficiency of electromicrobial protein production. This work provides a roadmap for development of engineered microbes that could significantly expand access to proteins produced with a low environmental footprint.
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Affiliation(s)
- Lucas Wise
- > Department of Food Sciences, Cornell University, Ithaca, NY, United States
| | - Sabrina Marecos
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Katie Randolph
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Mohamed Hassan
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Eric Nshimyumukiza
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Jacob Strouse
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Farshid Salimijazi
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Buz Barstow
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, United States
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40
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Adamson LSR, Tasneem N, Andreas MP, Close W, Jenner EN, Szyszka TN, Young R, Cheah LC, Norman A, MacDermott-Opeskin HI, O'Mara ML, Sainsbury F, Giessen TW, Lau YH. Pore structure controls stability and molecular flux in engineered protein cages. SCIENCE ADVANCES 2022. [PMID: 35119930 DOI: 10.1101/2021.01.27.428512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Protein cages are a common architectural motif used by living organisms to compartmentalize and control biochemical reactions. While engineered protein cages have featured in the construction of nanoreactors and synthetic organelles, relatively little is known about the underlying molecular parameters that govern stability and flux through their pores. In this work, we systematically designed 24 variants of the Thermotoga maritima encapsulin cage, featuring pores of different sizes and charges. Twelve pore variants were successfully assembled and purified, including eight designs with exceptional thermal stability. While negatively charged mutations were better tolerated, we were able to form stable assemblies covering a full range of pore sizes and charges, as observed in seven new cryo-EM structures at 2.5- to 3.6-Å resolution. Molecular dynamics simulations and stopped-flow experiments revealed the importance of considering both pore size and charge, together with flexibility and rate-determining steps, when designing protein cages for controlling molecular flux.
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Affiliation(s)
- Lachlan S R Adamson
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Nuren Tasneem
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Michael P Andreas
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - William Close
- Australian Centre for Microscopy and Microanalysis, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Eric N Jenner
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Taylor N Szyszka
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Reginald Young
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Li Chen Cheah
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 41 Boggo Road, Dutton Park, QLD 4102, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Alexander Norman
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Camperdown, NSW 2006, Australia
| | | | - Megan L O'Mara
- Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - Frank Sainsbury
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 41 Boggo Road, Dutton Park, QLD 4102, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | - Tobias W Giessen
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Camperdown, NSW 2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Campderdown, NSW 2006, Australia
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41
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Adamson LSR, Tasneem N, Andreas MP, Close W, Jenner EN, Szyszka TN, Young R, Cheah LC, Norman A, MacDermott-Opeskin HI, O’Mara ML, Sainsbury F, Giessen TW, Lau YH. Pore structure controls stability and molecular flux in engineered protein cages. SCIENCE ADVANCES 2022; 8:eabl7346. [PMID: 35119930 PMCID: PMC8816334 DOI: 10.1126/sciadv.abl7346] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Protein cages are a common architectural motif used by living organisms to compartmentalize and control biochemical reactions. While engineered protein cages have featured in the construction of nanoreactors and synthetic organelles, relatively little is known about the underlying molecular parameters that govern stability and flux through their pores. In this work, we systematically designed 24 variants of the Thermotoga maritima encapsulin cage, featuring pores of different sizes and charges. Twelve pore variants were successfully assembled and purified, including eight designs with exceptional thermal stability. While negatively charged mutations were better tolerated, we were able to form stable assemblies covering a full range of pore sizes and charges, as observed in seven new cryo-EM structures at 2.5- to 3.6-Å resolution. Molecular dynamics simulations and stopped-flow experiments revealed the importance of considering both pore size and charge, together with flexibility and rate-determining steps, when designing protein cages for controlling molecular flux.
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Affiliation(s)
- Lachlan S. R. Adamson
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Nuren Tasneem
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Michael P. Andreas
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - William Close
- Australian Centre for Microscopy and Microanalysis, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Eric N. Jenner
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Taylor N. Szyszka
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Reginald Young
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Li Chen Cheah
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 41 Boggo Road, Dutton Park, QLD 4102, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Alexander Norman
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Camperdown, NSW 2006, Australia
| | | | - Megan L. O’Mara
- Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - Frank Sainsbury
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 41 Boggo Road, Dutton Park, QLD 4102, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | - Tobias W. Giessen
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
- Corresponding author. (T.W.G.); (Y.H.L.)
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Camperdown, NSW 2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Campderdown, NSW 2006, Australia
- Corresponding author. (T.W.G.); (Y.H.L.)
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42
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Chen T, Fang Y, Jiang Q, Dykes GF, Lin Y, Price GD, Long BM, Liu LN. Incorporation of Functional Rubisco Activases into Engineered Carboxysomes to Enhance Carbon Fixation. ACS Synth Biol 2022; 11:154-161. [PMID: 34664944 PMCID: PMC8787814 DOI: 10.1021/acssynbio.1c00311] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
The carboxysome is
a versatile paradigm of prokaryotic organelles
and is a proteinaceous self-assembling microcompartment that plays
essential roles in carbon fixation in all cyanobacteria and some chemoautotrophs.
The carboxysome encapsulates
the central CO2-fixing enzyme, ribulose-1,5-bisphosphate
carboxylase/oxygenase (Rubisco), using a polyhedral protein shell
that is selectively permeable to specific metabolites in favor of
Rubisco carboxylation. There is tremendous interest in repurposing
carboxysomes to boost carbon fixation in heterologous organisms. Here,
we develop the design and engineering of α-carboxysomes by coexpressing
the Rubisco activase components CbbQ and CbbO with α-carboxysomes
in Escherichia coli. Our results show
that CbbQ and CbbO could assemble into the reconstituted α-carboxysome
as intrinsic components. Incorporation of both CbbQ and CbbO within
the carboxysome promotes activation of Rubisco and enhances the CO2-fixation activities of recombinant carboxysomes. We also
show that the structural composition of these carboxysomes could be
modified in different expression systems, representing the plasticity
of the carboxysome architecture. In translational terms, our study
informs strategies for engineering and modulating carboxysomes in
diverse biotechnological applications.
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Affiliation(s)
- Taiyu Chen
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Yi Fang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
| | - Qiuyao Jiang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
| | - Gregory F. Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - G. Dean Price
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory 2601, Australia
| | - Benedict M. Long
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory 2601, Australia
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
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43
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Hierarchically encapsulating enzymes with multi-shelled metal-organic frameworks for tandem biocatalytic reactions. Nat Commun 2022; 13:305. [PMID: 35027566 PMCID: PMC8758787 DOI: 10.1038/s41467-022-27983-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 12/10/2021] [Indexed: 01/25/2023] Open
Abstract
Biocatalytic transformations in living organisms, such as multi-enzyme catalytic cascades, proceed in different cellular membrane-compartmentalized organelles with high efficiency. Nevertheless, it remains challenging to mimicking biocatalytic cascade processes in natural systems. Herein, we demonstrate that multi-shelled metal-organic frameworks (MOFs) can be used as a hierarchical scaffold to spatially organize enzymes on nanoscale to enhance cascade catalytic efficiency. Encapsulating multi-enzymes with multi-shelled MOFs by epitaxial shell-by-shell overgrowth leads to 5.8~13.5-fold enhancements in catalytic efficiencies compared with free enzymes in solution. Importantly, multi-shelled MOFs can act as a multi-spatial-compartmental nanoreactor that allows physically compartmentalize multiple enzymes in a single MOF nanoparticle for operating incompatible tandem biocatalytic reaction in one pot. Additionally, we use nanoscale Fourier transform infrared (nano-FTIR) spectroscopy to resolve nanoscale heterogeneity of vibrational activity associated to enzymes encapsulated in multi-shelled MOFs. Furthermore, multi-shelled MOFs enable facile control of multi-enzyme positions according to specific tandem reaction routes, in which close positioning of enzyme-1-loaded and enzyme-2-loaded shells along the inner-to-outer shells could effectively facilitate mass transportation to promote efficient tandem biocatalytic reaction. This work is anticipated to shed new light on designing efficient multi-enzyme catalytic cascades to encourage applications in many chemical and pharmaceutical industrial processes. Mimicking multi-enzyme catalytic cascades in natural systems with spatial organization in confined structures is gaining increasing attention in the emerging field of systems chemistry. Here, the authors demonstrate that multi-shelled metal-organic frameworks can be used as a hierarchical scaffold to spatially organize enzymes on nanoscale to enhance cascade catalytic efficiency.
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44
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Baharifar H, Khoshnevisan K, Maleki H. Compartmentalized Immobilization of Multi-enzyme Systems. Methods Mol Biol 2022; 2487:151-162. [PMID: 35687234 DOI: 10.1007/978-1-0716-2269-8_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The methods of compartmentalized immobilization in multi-enzyme systems containing inorganic complexes and organic scaffolds (i.e. nucleic acid (RNA and DNA), protein and lipid) have been thoroughly investigated. Compartmentalization mostly focuses on dividing individual enzyme(s) into specific location or orientation of the enzymes cooperating in cascade reaction. Organic scaffolds are preferred because of their capability for simultaneous synthesis in biological systems. Besides, the most required methods of horseradish peroxidase (HRP) and glucose oxidase (GOD) enzymes including enzyme activity measurement, enzyme immobilization, removal, and re-hybridization, and enzyme attaching have been provided because they have been extensively applied in multi-enzyme systems. Organic scaffolds have a wide range and properties. Therefore, two methods including dockerin-cohesin linker and nucleotides interaction have been demonstrated for immobilization of enzyme on protein and DNA scaffold, respectively.
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Affiliation(s)
- Hadi Baharifar
- Department of Medical Nanotechnology, Applied Biophotonics Research Center, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Kamyar Khoshnevisan
- Medical Nanotechnology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Hassan Maleki
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
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45
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Yang X, Tan Z, Sun H, Tong Y, Huang X, Ren J, Wang C, Shen W. Fabrication of Hierarchical Nanoreactor based on COFs for Cascade Enzyme Catalysis. Chem Commun (Camb) 2022; 58:3933-3936. [DOI: 10.1039/d2cc00269h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A hierarchical nanoreactor based on covalent organic frameworks (COFs) was fabricated using polystyrene spheres (PSs) as template. When applied in cascade catalysis, the nanoreactor improved significantly the catalytic activity of...
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46
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Jolly BJ, Co NH, Davis AR, Diaconescu PL, Liu C. A generalized kinetic model for compartmentalization of organometallic catalysis. Chem Sci 2022; 13:1101-1110. [PMID: 35211276 PMCID: PMC8790775 DOI: 10.1039/d1sc04983f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/21/2021] [Indexed: 11/21/2022] Open
Abstract
Compartmentalization is an attractive approach to enhance catalytic activity by retaining reactive intermediates and mitigating deactivating pathways. Such a concept has been well explored in biochemical and more recently, organometallic catalysis to ensure high reaction turnovers with minimal side reactions. However, the scarcity of theoretical frameworks towards confined organometallic chemistry impedes broader utility for the implementation of compartmentalization. Herein, we report a general kinetic model and offer design guidance for a compartmentalized organometallic catalytic cycle. In comparison to a non-compartmentalized catalysis, compartmentalization is quantitatively shown to prevent the unwanted intermediate deactivation, boost the corresponding reaction efficiency (γ), and subsequently increase catalytic turnover frequency (TOF). The key parameter in the model is the volumetric diffusive conductance (FV) that describes catalysts' diffusion propensity across a compartment's boundary. Optimal values of FV for a specific organometallic chemistry are needed to achieve maximal values of γ and TOF. As illustrated in specific reaction examples, our model suggests that a tailored compartment design, including the use of nanomaterials, is needed to suit a specific organometallic catalytic cycle. This work provides justification and design principles for further exploration into compartmentalizing organometallics to enhance catalytic performance. The conclusions from this work are generally applicable to other catalytic systems that need proper design guidance in confinement and compartmentalization. Compartmentalization is an attractive approach to enhance catalytic activity by retaining reactive intermediates and mitigating deactivating pathways.![]()
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Affiliation(s)
- Brandon J. Jolly
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Nathalie H. Co
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Ashton R. Davis
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Paula L. Diaconescu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Chong Liu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA 90095, USA
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47
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Lian SWM, Guo S, Ren K, Xu Y, Ho JS, Chen CH. Heterogeneous multi-compartmental DNA hydrogel particles prepared via microfluidic assembly for lymphocyte-inspired precision medicine. NANOSCALE 2021; 13:20531-20540. [PMID: 34859803 DOI: 10.1039/d1nr06594g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Lymphocytes play a vital role in immunosurveillance through sensing biomolecules and eliminating targeted invaders. Compared with conventional therapies that depend on drug loading, lymphocytes are advantageous as they are able to ensure self-regulated therapeutics. Here, novel multi-compartmental DNA hydrogel particles were synthesized using a microfluidic assembly for intelligent cancer treatment via the logic-based control of siRNA release without external stimulation. The sensing sequence (D1) was compartmentalized from the treatment sequence (D2) with the use of core-shell DNA hydrogel particles. When D1 detects a cancer-associated biomarker, miRNA-21, a sequence cascade is triggered to release siRNA from D2, effectively eliminating the targeted cancer cells via lymphocyte-inspired precision medicine.
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Affiliation(s)
- Sophie Wan Mei Lian
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 04-08, 117583, Singapore
- Institute for Health Innovation and Technology (iHealthtech), MD6, 14 Medical Drive #14-01, Singapore 117599
| | - Song Guo
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 04-08, 117583, Singapore
- Institute for Health Innovation and Technology (iHealthtech), MD6, 14 Medical Drive #14-01, Singapore 117599
| | - Kewei Ren
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 04-08, 117583, Singapore
| | - Ying Xu
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China.
| | - John S Ho
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 04-08, 117583, Singapore
- Institute for Health Innovation and Technology (iHealthtech), MD6, 14 Medical Drive #14-01, Singapore 117599
| | - Chia-Hung Chen
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China.
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48
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Sustained enzymatic activity and flow in crowded protein droplets. Nat Commun 2021; 12:6293. [PMID: 34725341 PMCID: PMC8560906 DOI: 10.1038/s41467-021-26532-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/11/2021] [Indexed: 11/09/2022] Open
Abstract
Living cells harvest energy from their environments to drive the chemical processes that enable life. We introduce a minimal system that operates at similar protein concentrations, metabolic densities, and length scales as living cells. This approach takes advantage of the tendency of phase-separated protein droplets to strongly partition enzymes, while presenting minimal barriers to transport of small molecules across their interface. By dispersing these microreactors in a reservoir of substrate-loaded buffer, we achieve steady states at metabolic densities that match those of the hungriest microorganisms. We further demonstrate the formation of steady pH gradients, capable of driving microscopic flows. Our approach enables the investigation of the function of diverse enzymes in environments that mimic cytoplasm, and provides a flexible platform for studying the collective behavior of matter driven far from equilibrium.
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49
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Feng K, Gao N, Li W, Dong H, Sun F, He G, Zhou K, Zhao H, Li G. Arrested Coalescence of Ionic Liquid Droplets: A Facile Strategy for Spatially Organized Multicompartment Assemblies. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2104385. [PMID: 34643335 DOI: 10.1002/smll.202104385] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 09/01/2021] [Indexed: 06/13/2023]
Abstract
Multicompartment assemblies attract much attention for their wide applications. However, the fabrication of multicompartment assemblies usually requires elaborately designed building blocks and careful controlling. The emergence of droplet networks has provided a facile way to construct multiple droplet architectures, which can further be converted to multicompartment assemblies. Herein, the bind motif-free building blocks are presented, which consist of the hydrophobic Tf2 N- -based ionic liquid (IL) dissolving LiTf2 N salt, that can conjugate via arrested coalescence in confined-space templates to form IL droplet networks. Subsequent ultraviolent polymerization generates robust free-standing multicompartment assemblies. The conjugation of building blocks relies not on the peripheral bind motif but on the interfacial instability-induced arrested coalescence, avoiding tedious surface modification and assembly process. By tuning structures of templates and building blocks, multicompartment assemblies with 0D, 1D, 2D, and 3D structures are prepared in a facile and high-throughput way. Importantly, the bottom-up construction enables modular control over the compositions and spatial positions of individual building blocks. Combining with the excellent solvency of ILs, this system can serve as a general platform towards versatile multicompartment architectures. As demonstrations, by tailoring the chambers the multicompartment assemblies can spatiotemporally sense and report the chemical cues and perform various modes of motion.
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Affiliation(s)
- Kai Feng
- Department of Chemistry, Key Lab of Organic Optoelectronics & Molecular Engineering, Tsinghua University, Beijing, 100084, China
| | - Ning Gao
- Department of Chemistry, Key Lab of Organic Optoelectronics & Molecular Engineering, Tsinghua University, Beijing, 100084, China
| | - Wenyun Li
- Department of Chemistry, Key Lab of Organic Optoelectronics & Molecular Engineering, Tsinghua University, Beijing, 100084, China
| | - Hao Dong
- Department of Chemistry, Key Lab of Organic Optoelectronics & Molecular Engineering, Tsinghua University, Beijing, 100084, China
| | - Fuwei Sun
- Department of Chemistry, Key Lab of Organic Optoelectronics & Molecular Engineering, Tsinghua University, Beijing, 100084, China
| | - Guokang He
- Department of Chemistry, Key Lab of Organic Optoelectronics & Molecular Engineering, Tsinghua University, Beijing, 100084, China
| | - Kang Zhou
- Department of Chemistry, Key Lab of Organic Optoelectronics & Molecular Engineering, Tsinghua University, Beijing, 100084, China
| | - Hongwei Zhao
- Department of Chemistry, Key Lab of Organic Optoelectronics & Molecular Engineering, Tsinghua University, Beijing, 100084, China
| | - Guangtao Li
- Department of Chemistry, Key Lab of Organic Optoelectronics & Molecular Engineering, Tsinghua University, Beijing, 100084, China
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50
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Shetty S, Yandrapalli N, Pinkwart K, Krafft D, Vidakovic-Koch T, Ivanov I, Robinson T. Directed Signaling Cascades in Monodisperse Artificial Eukaryotic Cells. ACS NANO 2021; 15:15656-15666. [PMID: 34570489 PMCID: PMC8552445 DOI: 10.1021/acsnano.1c04219] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Indexed: 05/28/2023]
Abstract
The bottom-up assembly of multicompartment artificial cells that are able to direct biochemical reactions along a specific spatial pathway remains a considerable engineering challenge. In this work, we address this with a microfluidic platform that is able to produce monodisperse multivesicular vesicles (MVVs) to serve as synthetic eukaryotic cells. Using a two-inlet polydimethylsiloxane channel design to co-encapsulate different populations of liposomes we are able to produce lipid-based MVVs in a high-throughput manner and with three separate inner compartments, each containing a different enzyme: α-glucosidase, glucose oxidase, and horseradish peroxidase. We demonstrate the ability of these MVVs to carry out directed chemical communication between the compartments via the reconstitution of size-selective membrane pores. Therefore, the signal transduction, which is triggered externally, follows a specific spatial pathway between the compartments. We use this platform to study the effects of enzyme cascade compartmentalization by direct analytical comparison between bulk, one-, two-, and three-compartment systems. This microfluidic strategy to construct complex hierarchical structures is not only suitable to study compartmentalization effects on biochemical reactions but is also applicable for developing advanced drug delivery systems as well as minimal cells in the field of bottom-up synthetic biology.
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Affiliation(s)
- Sunidhi
C. Shetty
- Theory
and Bio-Systems, Max Planck Institute of
Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Naresh Yandrapalli
- Theory
and Bio-Systems, Max Planck Institute of
Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Kerstin Pinkwart
- Theory
and Bio-Systems, Max Planck Institute of
Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Dorothee Krafft
- Max
Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Tanja Vidakovic-Koch
- Max
Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Ivan Ivanov
- Max
Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Tom Robinson
- Theory
and Bio-Systems, Max Planck Institute of
Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
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