1
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Akter M, Moghimianavval H, Luker GD, Liu AP. Light-triggered protease-mediated release of actin-bound cargo from synthetic cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.15.613133. [PMID: 39314483 PMCID: PMC11419145 DOI: 10.1101/2024.09.15.613133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Synthetic cells offer a versatile platform for addressing biomedical and environmental challenges, due to their modular design and capability to mimic cellular processes such as biosensing, intercellular communication, and metabolism. Constructing synthetic cells capable of stimuli-responsive secretion is vital for applications in targeted drug delivery and biosensor development. Previous attempts at engineering secretion for synthetic cells have been confined to non-specific cargo release via membrane pores, limiting the spatiotemporal precision and specificity necessary for selective secretion. Here, we designed and constructed a protein-based platform termed TEV Protease-mediated Releasable Actin-binding protein (TRAP) for selective, rapid, and triggerable secretion in synthetic cells. TRAP is designed to bind tightly to reconstituted actin networks and is proteolytically released from bound actin, followed by secretion via cell-penetrating peptide membrane translocation. We demonstrated TRAP's efficacy in facilitating light-activated secretion of both fluorescent and luminescent proteins. By equipping synthetic cells with a controlled secretion mechanism, TRAP paves the way for the development of stimuli-responsive biomaterials, versatile synthetic cell-based biosensing systems, and therapeutic applications through the integration of synthetic cells with living cells for targeted delivery of protein therapeutics.
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Affiliation(s)
- Mousumi Akter
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Gary D. Luker
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Radiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Allen P. Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Biophysics, University of Michigan, Ann Arbor, MI, 48109, USA
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2
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Chen C, Ganar KA, de Haas RJ, Jarnot N, Hogeveen E, de Vries R, Deshpande S. Elastin-like polypeptide coacervates as reversibly triggerable compartments for synthetic cells. Commun Chem 2024; 7:198. [PMID: 39232074 PMCID: PMC11374812 DOI: 10.1038/s42004-024-01270-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 08/05/2024] [Indexed: 09/06/2024] Open
Abstract
Compartmentalization is a vital aspect of living cells to orchestrate intracellular processes. In a similar vein, constructing dynamic and responsive sub-compartments is key to synthetic cell engineering. In recent years, liquid-liquid phase separation via coacervation has offered an innovative avenue for creating membraneless organelles (MOs) within artificial cells. Here, we present a lab-on-a-chip system to reversibly trigger peptide-based coacervates within cell-mimicking confinements. We use double emulsion droplets (DEs) as our synthetic cell containers while pH-responsive elastin-like polypeptides (ELPs) act as the coacervate system. We first present a high-throughput microfluidic DE production enabling efficient encapsulation of the ELPs. The DEs are then harvested to perform multiple MO formation-dissolution cycles using pH as well as temperature variation. For controlled long-term visualization and modulation of the external environment, we developed an integrated microfluidic device for trapping and environmental stimulation of DEs, with negligible mechanical force, and demonstrated a proof-of-principle osmolyte-based triggering to induce multiple MO formation-dissolution cycles. In conclusion, our work showcases the use of DEs and ELPs in designing membraneless reversible compartmentalization within synthetic cells via physicochemical triggers. Additionally, presented on-chip platform can be applied over a wide range of phase separation and vesicle systems for applications in synthetic cells and beyond.
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Affiliation(s)
- Chang Chen
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Ketan A Ganar
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Robbert J de Haas
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Nele Jarnot
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Erwin Hogeveen
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Renko de Vries
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Siddharth Deshpande
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
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3
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Rothschild LJ, Averesch NJH, Strychalski EA, Moser F, Glass JI, Cruz Perez R, Yekinni IO, Rothschild-Mancinelli B, Roberts Kingman GA, Wu F, Waeterschoot J, Ioannou IA, Jewett MC, Liu AP, Noireaux V, Sorenson C, Adamala KP. Building Synthetic Cells─From the Technology Infrastructure to Cellular Entities. ACS Synth Biol 2024; 13:974-997. [PMID: 38530077 PMCID: PMC11037263 DOI: 10.1021/acssynbio.3c00724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 03/27/2024]
Abstract
The de novo construction of a living organism is a compelling vision. Despite the astonishing technologies developed to modify living cells, building a functioning cell "from scratch" has yet to be accomplished. The pursuit of this goal alone has─and will─yield scientific insights affecting fields as diverse as cell biology, biotechnology, medicine, and astrobiology. Multiple approaches have aimed to create biochemical systems manifesting common characteristics of life, such as compartmentalization, metabolism, and replication and the derived features, evolution, responsiveness to stimuli, and directed movement. Significant achievements in synthesizing each of these criteria have been made, individually and in limited combinations. Here, we review these efforts, distinguish different approaches, and highlight bottlenecks in the current research. We look ahead at what work remains to be accomplished and propose a "roadmap" with key milestones to achieve the vision of building cells from molecular parts.
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Affiliation(s)
- Lynn J. Rothschild
- Space Science
& Astrobiology Division, NASA Ames Research
Center, Moffett
Field, California 94035-1000, United States
- Department
of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Nils J. H. Averesch
- Department
of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | | | - Felix Moser
- Synlife, One Kendall Square, Cambridge, Massachusetts 02139-1661, United States
| | - John I. Glass
- J.
Craig
Venter Institute, La Jolla, California 92037, United States
| | - Rolando Cruz Perez
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
- Blue
Marble
Space Institute of Science at NASA Ames Research Center, Moffett Field, California 94035-1000, United
States
| | - Ibrahim O. Yekinni
- Department
of Biomedical Engineering, University of
Minnesota, Minneapolis, Minnesota 55455, United States
| | - Brooke Rothschild-Mancinelli
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332-0150, United States
| | | | - Feilun Wu
- J. Craig
Venter Institute, Rockville, Maryland 20850, United States
| | - Jorik Waeterschoot
- Mechatronics,
Biostatistics and Sensors (MeBioS), KU Leuven, 3000 Leuven Belgium
| | - Ion A. Ioannou
- Department
of Chemistry, MSRH, Imperial College London, London W12 0BZ, U.K.
| | - Michael C. Jewett
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Allen P. Liu
- Mechanical
Engineering & Biomedical Engineering, Cellular and Molecular Biology,
Biophysics, Applied Physics, University
of Michigan, Ann Arbor, Michigan 48109, United States
| | - Vincent Noireaux
- Physics
and Nanotechnology, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Carlise Sorenson
- Department
of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Katarzyna P. Adamala
- Department
of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States
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4
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Jones JA, Andreas MP, Giessen TW. Structural basis for peroxidase encapsulation inside the encapsulin from the Gram-negative pathogen Klebsiella pneumoniae. Nat Commun 2024; 15:2558. [PMID: 38519509 PMCID: PMC10960027 DOI: 10.1038/s41467-024-46880-x] [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: 09/21/2023] [Accepted: 03/12/2024] [Indexed: 03/25/2024] Open
Abstract
Encapsulins are self-assembling protein nanocompartments capable of selectively encapsulating dedicated cargo proteins, including enzymes involved in iron storage, sulfur metabolism, and stress resistance. They represent a unique compartmentalization strategy used by many pathogens to facilitate specialized metabolic capabilities. Encapsulation is mediated by specific cargo protein motifs known as targeting peptides (TPs), though the structural basis for encapsulation of the largest encapsulin cargo class, dye-decolorizing peroxidases (DyPs), is currently unknown. Here, we characterize a DyP-containing encapsulin from the enterobacterial pathogen Klebsiella pneumoniae. By combining cryo-electron microscopy with TP and TP-binding site mutagenesis, we elucidate the molecular basis for cargo encapsulation. TP binding is mediated by cooperative hydrophobic and ionic interactions as well as shape complementarity. Our results expand the molecular understanding of enzyme encapsulation inside protein nanocompartments and lay the foundation for rationally modulating encapsulin cargo loading for biomedical and biotechnological applications.
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Affiliation(s)
- Jesse A Jones
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Michael P Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Tobias W Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA.
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5
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Moghimianavval H, Mohapatra S, Liu AP. A Mammalian-Based Synthetic Biology Toolbox to Engineer Membrane-Membrane Interfaces. Methods Mol Biol 2024; 2774:43-58. [PMID: 38441757 DOI: 10.1007/978-1-0716-3718-0_4] [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: 03/07/2024]
Abstract
Intercellular membrane-membrane interfaces are compartments with specialized functions and unique biophysical properties that are essential in numerous cellular processes including cell signaling, development, and immunity. Using synthetic biology to engineer or to create novel cellular functions in the intercellular regions has led to an increasing need for a platform that allows generation of functionalized intercellular membrane-membrane interfaces. Here, we present a synthetic biology platform to engineer functional membrane-membrane interfaces using a pair of dimerizing proteins in both cell-free and cellular environments. We envisage this platform to be a helpful tool for synthetic biologists who wish to engineer novel intercellular signaling and communication systems.
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Affiliation(s)
| | - Sonisilpa Mohapatra
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Allen P Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA.
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA.
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA.
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6
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de Haas R, Ganar KA, Deshpande S, de Vries R. pH-Responsive Elastin-Like Polypeptide Designer Condensates. ACS APPLIED MATERIALS & INTERFACES 2023; 15:45336-45344. [PMID: 37707425 PMCID: PMC10540133 DOI: 10.1021/acsami.3c11314] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/01/2023] [Indexed: 09/15/2023]
Abstract
Biomolecular condensates are macromolecular complexes formed by liquid-liquid phase separation. They regulate key biological functions by reversibly compartmentalizing molecules in cells, in a stimulus-dependent manner. Designing stimuli-responsive synthetic condensates is crucial for engineering compartmentalized synthetic cells that are able to mimic spatiotemporal control over the biochemical reactions. Here, we design and test a family of condensate-forming, pH-responsive elastin-like polypeptides (ELPs) that form condensates above critical pH values ranging between 4 and 7, for temperatures between 20 and at 37 °C. We show that the condensation occurs rapidly, in sharp pH intervals (ΔpH < 0.3). For eventual applications in engineering synthetic cell compartments, we demonstrate that multiple types of pH-responsive ELPs can form mixed condensates inside micron-sized vesicles. When genetically fused with enzymes, receptors, and signaling molecules, these pH-responsive ELPs could be potentially used as pH-switchable functional condensates for spatially controlling biochemistry in engineered synthetic cells.
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Affiliation(s)
- Robbert
J. de Haas
- Department of Physical Chemistry
and Soft Matter, Wageningen University and
Research, 6708 WE Wageningen, The Netherlands
| | - Ketan A. Ganar
- Department of Physical Chemistry
and Soft Matter, Wageningen University and
Research, 6708 WE Wageningen, The Netherlands
| | - Siddharth Deshpande
- Department of Physical Chemistry
and Soft Matter, Wageningen University and
Research, 6708 WE Wageningen, The Netherlands
| | - Renko de Vries
- Department of Physical Chemistry
and Soft Matter, Wageningen University and
Research, 6708 WE Wageningen, The Netherlands
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7
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Jones JA, Andreas MP, Giessen TW. Structural basis for peroxidase encapsulation in a protein nanocompartment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558302. [PMID: 37790520 PMCID: PMC10542125 DOI: 10.1101/2023.09.18.558302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Encapsulins are self-assembling protein nanocompartments capable of selectively encapsulating dedicated cargo proteins, including enzymes involved in iron storage, sulfur metabolism, and stress resistance. They represent a unique compartmentalization strategy used by many pathogens to facilitate specialized metabolic capabilities. Encapsulation is mediated by specific cargo protein motifs known as targeting peptides (TPs), though the structural basis for encapsulation of the largest encapsulin cargo class, dye-decolorizing peroxidases (DyPs), is currently unknown. Here, we characterize a DyP-containing encapsulin from the enterobacterial pathogen Klebsiella pneumoniae. By combining cryo-electron microscopy with TP mutagenesis, we elucidate the molecular basis for cargo encapsulation. TP binding is mediated by cooperative hydrophobic and ionic interactions as well as shape complementarity. Our results expand the molecular understanding of enzyme encapsulation inside protein nanocompartments and lay the foundation for rationally modulating encapsulin cargo loading for biomedical and biotechnological applications.
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Affiliation(s)
- Jesse A. Jones
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Michael P. Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Tobias W. Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
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8
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Allen ME, Hindley JW, O’Toole N, Cooke HS, Contini C, Law RV, Ces O, Elani Y. Biomimetic behaviors in hydrogel artificial cells through embedded organelles. Proc Natl Acad Sci U S A 2023; 120:e2307772120. [PMID: 37603747 PMCID: PMC10466294 DOI: 10.1073/pnas.2307772120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/13/2023] [Indexed: 08/23/2023] Open
Abstract
Artificial cells are biomimetic structures formed from molecular building blocks that replicate biological processes, behaviors, and architectures. Of these building blocks, hydrogels have emerged as ideal, yet underutilized candidates to provide a gel-like chassis in which to incorporate both biological and nonbiological componentry which enables the replication of cellular functionality. Here, we demonstrate a microfluidic strategy to assemble biocompatible cell-sized hydrogel-based artificial cells with a variety of different embedded functional subcompartments, which act as engineered synthetic organelles. The organelles enable the recreation of increasingly biomimetic behaviors, including stimulus-induced motility, content release through activation of membrane-associated proteins, and enzymatic communication with surrounding bioinspired compartments. In this way, we showcase a foundational strategy for the bottom-up construction of hydrogel-based artificial cell microsystems which replicate fundamental cellular behaviors, paving the way for the construction of next-generation biotechnological devices.
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Affiliation(s)
- Matthew E. Allen
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
- Department of Chemical Engineering, Imperial College London, South Kensington, LondonSW7 2AZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - James W. Hindley
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - Nina O’Toole
- Department of Chemical Engineering, Imperial College London, South Kensington, LondonSW7 2AZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - Hannah S. Cooke
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
- Department of Chemical Engineering, Imperial College London, South Kensington, LondonSW7 2AZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - Claudia Contini
- Department of Chemical Engineering, Imperial College London, South Kensington, LondonSW7 2AZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - Robert V. Law
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - Oscar Ces
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - Yuval Elani
- Department of Chemical Engineering, Imperial College London, South Kensington, LondonSW7 2AZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
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9
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Moghimianavval H, Patel C, Mohapatra S, Hwang SW, Kayikcioglu T, Bashirzadeh Y, Liu AP, Ha T. Engineering Functional Membrane-Membrane Interfaces by InterSpy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2202104. [PMID: 35618485 PMCID: PMC9789529 DOI: 10.1002/smll.202202104] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/26/2022] [Indexed: 06/15/2023]
Abstract
Engineering synthetic interfaces between membranes has potential applications in designing non-native cellular communication pathways and creating synthetic tissues. Here, InterSpy is introduced as a synthetic biology tool consisting of a heterodimeric protein engineered to form and maintain membrane-membrane interfaces between apposing synthetic as well as cell membranes through the SpyTag/SpyCatcher interaction. The inclusion of split fluorescent protein fragments in InterSpy allows tracking of the formation of a membrane-membrane interface and reconstitution of functional fluorescent protein in the space between apposing membranes. First, InterSpy is demonstrated by testing split protein designs using a mammalian cell-free expression (CFE) system. By utilizing co-translational helix insertion, cell-free synthesized InterSpy fragments are incorporated into the membrane of liposomes and supported lipid bilayers with the desired topology. Functional reconstitution of split fluorescent protein between the membranes is strictly dependent on SpyTag/SpyCatcher. Finally, InterSpy is demonstrated in mammalian cells by detecting fluorescence reconstitution of split protein at the membrane-membrane interface between two cells each expressing a component of InterSpy. InterSpy demonstrates the power of CFE systems in the functional reconstitution of synthetic membrane interfaces via proximity-inducing proteins. This technology may also prove useful where cell-cell contacts and communication are recreated in a controlled manner using minimal components.
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Affiliation(s)
- Hossein Moghimianavval
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Chintan Patel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sonisilpa Mohapatra
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sung-Won Hwang
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Tunc Kayikcioglu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Yashar Bashirzadeh
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Allen P. Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Baltimore, MD 21205, USA
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10
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Kwon S, Giessen TW. Engineered Protein Nanocages for Concurrent RNA and Protein Packaging In Vivo. ACS Synth Biol 2022; 11:3504-3515. [PMID: 36170610 PMCID: PMC9944510 DOI: 10.1021/acssynbio.2c00391] [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] [Indexed: 01/31/2023]
Abstract
Protein nanocages have emerged as an important engineering platform for biotechnological and biomedical applications. Among naturally occurring protein cages, encapsulin nanocompartments have recently gained prominence due to their favorable physico-chemical properties, ease of shell modification, and highly efficient and selective intrinsic protein packaging capabilities. Here, we expand encapsulin function by designing and characterizing encapsulins for concurrent RNA and protein encapsulation in vivo. Our strategy is based on modifying encapsulin shells with nucleic acid-binding peptides without disrupting the native protein packaging mechanism. We show that our engineered encapsulins reliably self-assemble in vivo, are capable of efficient size-selective in vivo RNA packaging, can simultaneously load multiple functional RNAs, and can be used for concurrent in vivo packaging of RNA and protein. Our engineered encapsulation platform has potential for codelivery of therapeutic RNAs and proteins to elicit synergistic effects and as a modular tool for other biotechnological applications.
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Affiliation(s)
- Seokmu Kwon
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Tobias W. Giessen
- Department of Biological Chemistry and Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
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11
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Majumder S, Hsu YY, Moghimianavval H, Andreas M, Giessen TW, Luxton GG, Liu AP. In Vitro Synthesis and Reconstitution Using Mammalian Cell-Free Lysates Enables the Systematic Study of the Regulation of LINC Complex Assembly. Biochemistry 2022; 61:1495-1507. [PMID: 35737522 PMCID: PMC9789527 DOI: 10.1021/acs.biochem.2c00118] [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] [Indexed: 01/31/2023]
Abstract
Understanding the structure and structure-function relationships of membrane proteins is a fundamental problem in biomedical research. Given the difficulties inherent to performing mechanistic biochemical and biophysical studies of membrane proteins in vitro, we previously developed a facile HeLa cell-based cell-free expression (CFE) system that enables the efficient reconstitution of full-length (FL) functional inner nuclear membrane Sad1/UNC-84 (SUN) proteins (i.e., SUN1 and SUN2) in supported lipid bilayers. Here, we provide evidence that suggests that the reconstitution of CFE-synthesized FL membrane proteins in supported lipid bilayers occurs primarily through the fusion of endoplasmic reticulum-derived microsomes present within our CFE reactions with our supported lipid bilayers. In addition, we demonstrate the ease with which our synthetic biology platform can be used to investigate the impact of the chemical environment on the ability of CFE-synthesized FL SUN proteins reconstituted in supported lipid bilayers to interact with the luminal domain of the KASH protein nesprin-2. Moreover, we use our platform to study the molecular requirements for the homo- and heterotypic interactions between SUN1 and SUN2. Finally, we show that our platform can be used to simultaneously reconstitute three different CFE-synthesized FL membrane proteins in a single supported lipid bilayer. Overall, these results establish our HeLa cell-based CFE and supported lipid bilayer reconstitution platform as a powerful tool for performing mechanistic dissections of the oligomerization and function of FL membrane proteins in vitro. While our platform is not a substitute for cell-based studies, it does provide important mechanistic insights into the biology of difficult-to-study membrane proteins.
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Affiliation(s)
- Sagardip Majumder
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Yen-Yu Hsu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Hossein Moghimianavval
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Michael Andreas
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Tobias W. Giessen
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - G.W. Gant Luxton
- Department of Molecular and Cellular Biology, University of California-Davis, Davis, California, 95616, USA
| | - Allen P. Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, Michigan, 48109, USA
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, 48109, USA
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12
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Moghimianavval H, Hsu YY, Groaz A, Liu AP. In Vitro Reconstitution Platforms of Mammalian Cell-Free Expressed Membrane Proteins. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2433:105-120. [PMID: 34985740 DOI: 10.1007/978-1-0716-1998-8_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Membrane proteins are essential components in cell membranes and enable cells to communicate with their outside environment and to carry out intracellular signaling. Functional reconstitution of complex membrane proteins using cell-free expression (CFE) systems has been proved to be challenging mainly due to the lack of necessary machinery for proper folding and translocation of nascent membrane proteins and their delivery to the supplied synthetic bilayers. Here, we provide protocols for detergent-free, cell-free reconstitution of functional membrane proteins using HeLa-based CFE system and outline assays for studying their membrane insertion, topology, and their orientation upon incorporation into the supported lipid bilayers or bilayers of giant unilamellar vesicles as well as methods to isolate functional translocated cell-free produced membrane proteins.
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Affiliation(s)
| | - Yen-Yu Hsu
- University of Michigan, Ann Arbor, MI, USA
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13
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Wen P, Wang X, Chen H, Appelhans D, Liu X, Wang L, Huang X. A
pH Self‐Monitoring
Heterogeneous Multicompartmental Proteinosome with Spatiotemporal Regulation of Insulin Transportation. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202100519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Ping Wen
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage School of Chemistry and Chemical Engineering, Harbin Institute of Technology (HIT), Harbin Heilongjiang 150001 China
| | - Xueyi Wang
- Dongguan Hospital of Southern Medical University, Southern Medical University Dongguan Guangdong 523059 China
| | - Haixu Chen
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage School of Chemistry and Chemical Engineering, Harbin Institute of Technology (HIT), Harbin Heilongjiang 150001 China
| | - Dietmar Appelhans
- Leibniz‐Institut für Polymerforschung Dresden e.V., Hohe Straße 6 Dresden 01069 Germany
| | - Xiaoman Liu
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage School of Chemistry and Chemical Engineering, Harbin Institute of Technology (HIT), Harbin Heilongjiang 150001 China
| | - Lei Wang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage School of Chemistry and Chemical Engineering, Harbin Institute of Technology (HIT), Harbin Heilongjiang 150001 China
| | - Xin Huang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage School of Chemistry and Chemical Engineering, Harbin Institute of Technology (HIT), Harbin Heilongjiang 150001 China
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Sharma B, Moghimianavval H, Hwang SW, Liu AP. Synthetic Cell as a Platform for Understanding Membrane-Membrane Interactions. MEMBRANES 2021; 11:912. [PMID: 34940413 PMCID: PMC8706075 DOI: 10.3390/membranes11120912] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/10/2021] [Accepted: 11/16/2021] [Indexed: 01/27/2023]
Abstract
In the pursuit of understanding life, model membranes made of phospholipids were envisaged decades ago as a platform for the bottom-up study of biological processes. Micron-sized lipid vesicles have gained great acceptance as their bilayer membrane resembles the natural cell membrane. Important biological events involving membranes, such as membrane protein insertion, membrane fusion, and intercellular communication, will be highlighted in this review with recent research updates. We will first review different lipid bilayer platforms used for incorporation of integral membrane proteins and challenges associated with their functional reconstitution. We next discuss different methods for reconstitution of membrane fusion and compare their fusion efficiency. Lastly, we will highlight the importance and challenges of intercellular communication between synthetic cells and synthetic cells-to-natural cells. We will summarize the review by highlighting the challenges and opportunities associated with studying membrane-membrane interactions and possible future research directions.
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Affiliation(s)
- Bineet Sharma
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; (B.S.); (H.M.)
| | - Hossein Moghimianavval
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; (B.S.); (H.M.)
| | - Sung-Won Hwang
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Allen P. Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; (B.S.); (H.M.)
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48105, USA
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48105, USA
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15
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Bashirzadeh Y, Wubshet N, Litschel T, Schwille P, Liu AP. Rapid Encapsulation of Reconstituted Cytoskeleton Inside Giant Unilamellar Vesicles. J Vis Exp 2021:10.3791/63332. [PMID: 34842240 PMCID: PMC8889913 DOI: 10.3791/63332] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Giant unilamellar vesicles (GUVs) are frequently used as models of biological membranes and thus are a great tool to study membrane-related cellular processes in vitro. In recent years, encapsulation within GUVs has proven to be a helpful approach for reconstitution experiments in cell biology and related fields. It better mimics confinement conditions inside living cells, as opposed to conventional biochemical reconstitution. Methods for encapsulation inside GUVs are often not easy to implement, and success rates can differ significantly from lab to lab. One technique that has proven to be successful for encapsulating more complex protein systems is called continuous droplet interface crossing encapsulation (cDICE). Here, a cDICE-based method is presented for rapidly encapsulating cytoskeletal proteins in GUVs with high encapsulation efficiency. In this method, first, lipid-monolayer droplets are generated by emulsifying a protein solution of interest in a lipid/oil mixture. After being added into a rotating 3D-printed chamber, these lipid-monolayered droplets then pass through a second lipid monolayer at a water/oil interface inside the chamber to form GUVs that contain the protein system. This method simplifies the overall procedure of encapsulation within GUVs and speeds up the process, and thus allows us to confine and observe the dynamic evolution of network assembly inside lipid bilayer vesicles. This platform is handy for studying the mechanics of cytoskeleton-membrane interactions in confinement.
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Affiliation(s)
| | - Nadab Wubshet
- Department of Mechanical Engineering, University of Michigan, Ann Arbor
| | - Thomas Litschel
- John A. Paulson School of Engineering and Applied Sciences, Harvard University
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry
| | - Allen P Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor; Department of Biomedical Engineering, University of Michigan, Ann Arbor; Department of Biophysics, University of Michigan, Ann Arbor; Cellular and Molecular Biology Program, University of Michigan, Ann Arbor;
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