Synthetic Organelles Research Articles

Peptide-Induced Division of Polymersomes for Biomimetic Compartmentalization.

Polymersomes are synthetic vesicles that mimic the architecture of cellular compartments such as the cell membrane and organelles. These biomimetic compartments facilitate the creation of cell-like chemical systems, including microreactors and synthetic organelles. However, the construction of hierarchical multi-compartment systems remains challenging and typically requires the encapsulation of pre-formed vesicles within a host compartment. Here, we report the formation of multicompartment polymersomes with a vesicle-in-vesicle architecture achieved through self-division induced by short peptides incorporated into the vesicle membrane. A phenylalanine-phenylalanine-methionine (FFM) tripeptide was designed and encapsulated into the polymersome via microfluidics. We demonstrate that vesicle self-division occurs due to peptide incorporation into the membrane in response to pH changes. This self-division creates internal vesicles capable of colocalizing enzymes. The hybrid polymer-peptide system described here provides a straightforward method for developing subcompartmentalized systems, paving the way for engineering microreactors with life-like properties.

Towards Synthetic Cells with Self-Producing Energy.

Autonomous generation of energy, specifically adenosine triphosphate (ATP), is critical for sustaining the engineered functionalities of synthetic cells constructed from the bottom-up. In this mini-review, we categorize studies on ATP-producing synthetic cells into three different approaches: photosynthetic mechanisms, mitochondrial respiration mimicry, and utilization of non-conventional approaches such as exploiting synthetic metabolic pathways. Within this framework, we evaluate the strengths and limitations of each approach and provide directions for future research endeavors. We also introduce a concept of building ATP-generating synthetic organelle that will enable us to mimic cellular respiration in a simpler way than current strategies. This review aims to highlight the importance of energy self-production in synthetic cells, providing suggestions and ideas that may help overcome some longstanding challenges in this field.

Co-transcriptional production of programmable RNA condensates and synthetic organelles.

Condensation of RNA and proteins is central to cellular functions, and the ability to program it would be valuable in synthetic biology and synthetic cell science. Here we introduce a modular platform for engineering synthetic RNA condensates from tailor-made, branched RNA nanostructures that fold and assemble co-transcriptionally. Up to three orthogonal condensates can form simultaneously and selectively accumulate fluorophores through embedded fluorescent light-up aptamers. The RNA condensates can be expressed within synthetic cells to produce membrane-less organelles with a controlled number and relative size, and showing the ability to capture proteins using selective protein-binding aptamers. The affinity between otherwise orthogonal nanostructures can be modulated by introducing dedicated linker constructs, enabling the production of bi-phasic RNA condensates with a prescribed degree of interphase mixing and diverse morphologies. The in situ expression of programmable RNA condensates could underpin the spatial organization of functionalities in both biological and synthetic cells.

Enhanced Catalytic Activity of a de novo Enzyme in a Coacervate Phase

Biomolecular condensates are membraneless organelles that orchestrate various metabolic pathways in living cells. Understanding how these crowded structures regulate enzyme reactions remains yet challenging due to their dynamic and intricate nature. Coacervate microdroplets formed by associative liquid‐liquid phase separation of oppositely charged polyions have emerged as relevant condensate models to study enzyme catalysis. Enzyme reactions within these droplets show altered kinetics, influenced by factors such as enzyme and substrate partitioning, crowding, and interactions with coacervate components; it is often challenging to disentangle the contributions of each. Here, we investigate the peroxidase activity of a de novo enzyme within polysaccharide‐based coacervates. By comparing the reaction kinetics in buffer, in a suspension of coacervates and in the bulk coacervate phase collected after centrifugation of the droplets, we show that the coacervate phase significantly increases the enzyme catalytic efficiency. We demonstrate that the main origin of this enhanced activity lies in macromolecular crowding coupled to changes in the conformational dynamics of the enzyme within the coacervate environment. Altogether, these findings underline the crucial role of the coacervate matrix in enzyme catalysis, beyond simple partitioning effects. The observed boost in enzyme activity within the coacervate phase provides insights for designing biocatalytically active synthetic organelles.

Biomimetic behaviors in hydrogel artificial cells through embedded organelles

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.

Sponge-phase Lipid Droplets as Synthetic Organelles: An Ultrafast Study of Hydrogen Bonding and Interfacial Environments.

Bottom-up design of biomimetic organelles has gained recent attention as a route towards understanding the transition between non-living matter and life. Despite various artificial lipid membranes being developed, the specific relations between lipid structure, composition, interfacial properties, and morphology are not currently understood. Sponge-phase droplets contain dense, nonlamellar lipid bilayer networks that capture the complexities of the endoplasmic reticulum (ER), making them ideal artificial models of such organelles. Here, we combine ultrafast two-dimensional infrared (2D IR) spectroscopy and molecular dynamics simulations to investigate the interfacial H-bond networks in sponge-phase droplets composed of glycolipid and nonionic detergents. In the sponge phase, the interfacial environments are more hydrated and water molecules confined to the nanometer-scale aqueous channels in the sponge phase exhibit dynamics that are significantly slower compared to bulk water. Surfactant configurations and microscopic phase separation play a dominant role in determining membrane curvature and slow dynamics observed in the sponge phase. The studies suggest that H-bond networks within the nanometer-scale channels are disrupted not only by confinement but also by the interactions of surfactants, which extend 1-2 nm from the bilayer surface. The results provide a molecular-level description for controlling phase and morphology in the design of synthetic lipid organelles.

Elucidating the Morphology of the Endoplasmic Reticulum: Puzzles and Perspectives.

Artificial or synthetic organelles are a key challenge for bottom-up synthetic biology. So far, synthetic organelles have typically been based on spherical membrane compartments, used to spatially confine selected chemical reactions. In vivo, these compartments are often far from being spherical and can exhibit rather complex architectures. A particularly fascinating example is provided by the endoplasmic reticulum (ER), which extends throughout the whole cell by forming a continuous network of membrane nanotubes connected by three-way junctions. The nanotubes have a typical diameter of between 50 and 100 nm. In spite of much experimental progress, several fundamental aspects of the ER morphology remain elusive. A long-standing puzzle is the straight appearance of the tubules in the light microscope, which form irregular polygons with contact angles close to 120°. Another puzzling aspect is the nanoscopic shapes of the tubules and junctions, for which very different images have been obtained by electron microcopy and structured illumination microscopy. Furthermore, both the formation and maintenance of the reticular networks require GTP and GTP-hydrolyzing membrane proteins. In fact, the networks are destroyed by the fragmentation of nanotubes when the supply of GTP is interrupted. Here, it is argued that all of these puzzling observations are intimately related to each other and to the dimerization of two membrane proteins anchored to the same membrane. So far, the functional significance of this dimerization process remained elusive and, thus, seemed to waste a lot of GTP. However, this process can generate an effective membrane tension that stabilizes the irregular polygonal geometry of the reticular networks and prevents the fragmentation of their tubules, thereby maintaining the integrity of the ER. By incorporating the GTP-hydrolyzing membrane proteins into giant unilamellar vesicles, the effective membrane tension will become accessible to systematic experimental studies.

Biomimetic Cell Structures: Probing Induced pH-Feedback Loops and pH Self-Monitoring in Cytosol Using Binary Enzyme-Loaded Polymersomes in Proteinosome.

Structures and functions of eukaryotic cells with an outer permeable membrane, a cytoskeleton, functional organelles, and motility can be mimicked by giant multicompartment protocells containing various synthetic organelles. Herein, two kinds of artificial organelles with stimuli-triggered regulation ability, glucose oxidase-(GOx)-loaded pH-responsive polymersomes A (GOx-Psomes A) and urease-loaded pH-responsive polymersomes B (Urease-Psomes B), and a pH-sensor (Dextran-FITC) are encapsulated into proteinosomes via the Pickering emulsion method. Thus, a polymersomes-in-proteinosome system is constructed which is able to probe biomimetic pH homeostasis. Alternating fuels (glucose or urea) introduced from outside the protocell penetrate the membrane of proteinosomes and enter into GOx-Psomes A and Urease-Psomes B to produce chemical signals (gluconic acid or ammonia) resulting in pH-feedback loops (pH jump and pH drop). This will counteract the catalytic "switch on" or "switch off" of enzyme-loaded Psomes A and B owing to their different pH-responsive membranes. Dextran-FITC in the proteinosome allows self-monitoring of slight pH fluctuations in the lumen of protocells. Overall, this approach shows heterogeneous polymersome-in-proteinosome architectures with sophisticated features such as input-regulated pH changes mediated by negative and positive feedback in loops and cytosolic pH self-monitoring, features that are imperative for advanced protocell design.

Phase-Separated Synthetic Organelles Based on Intrinsically Disordered Protein Domain for Metabolic Pathway Assembly in Escherichia coli.

Extensive research efforts have been focused on spatial organization of biocatalytic cascades or catalytic networks in confined cellular environments. Inspired by the natural metabolic systems that spatially regulate pathways via sequestration into subcellular compartments, formation of artificial membraneless organelles through expressing intrinsically disordered proteins in host strains has been proven to be a feasible strategy. Here we report the engineering of a synthetic membraneless organelle platform, which can be used to extend compartmentalization and spatially organize pathway sequential enzymes. We show that heterologous overexpression of the RGG domain derived from the disordered P granule protein LAF-1 in an Escherichia coli strain can form intracellular protein condensates via liquid-liquid phase separation. We further demonstrate that different clients can be recruited to the synthetic compartments via directly fusing with the RGG domain or cooperating with different protein interaction motifs. Using the 2'-fucosyllactose de novo biosynthesis pathway as a model system, we show that clustering sequential enzymes into synthetic compartments can effectively increase the titer and yield of the target product compared to strains with free-floating pathway enzymes. The synthetic membraneless organelle system constructed here gives a promising approach in the development of microbial cell factories, wherein it could be used for the compartmentalization of pathway enzymes to streamline metabolic flux.

Synthetic Multienzyme Assemblies for Natural Product Biosynthesis.

In nature, enzymes that catalyze sequential reactions are often assembled as clusters or complexes. The formation of multienzyme complexes, or metabolons, brings the enzyme active sites into proximity to promote intermediate transfer, decrease intermediate leakage, and streamline the metabolic flux towards the desired products. We and others have developed synthetic versions of metabolons through various strategies to enhance the catalytic rates for synthesizing valuable chemicals inside microbes. Synthetic multienzyme complexes range from static enzyme nanostructures to dynamic enzyme coacervates. Enzyme complexation optimizes the metabolic fluxes inside microbes, increases the product titer, and supplies the field with high-yield microbe strains that are amenable to large-scale fermentation. Enzyme complexes constructed inside microbial cells can be separated as independent entities and catalyze biosynthetic reactions ex vivo; such a feature gains these complexes another name, "synthetic organelles" - new subcellular entities with independent structures and functions. Still, the field is seeking new strategies to better balance dynamicity and confinement and to achieve finer control of local compartmentalization in the cells, as the natural multienzyme complexes do. Industrial applications of synthetic multienzyme complexes for the large-scale production of valuable chemicals are yet to be realized. This review focuses on synthetic multienzyme complexes that are constructed and function inside microbial cells.

A synthetic organelle approach to probe SNARE-mediated membrane fusion in a bacterial host

Invivo and invitro 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.

Abstract 2448: Evaluation of peroxisome size regulation through optogenetic enlargement for future use as synthetic organelle in Saccharomyces cerevisiae

Abstract 2448: Evaluation of peroxisome size regulation through optogenetic enlargement for future use as synthetic organelle in Saccharomyces cerevisiae

Synthetic Organelles for Multiple mRNA Selective Genetic Code Expansions in Eukaryotes.

Engineering new functionalities into living eukaryotic systems is one of the main goals of synthetic biology. To this end, often enzyme evolution or de novo protein design is employed, whicheach have their own advantages and disadvantages. As complimentary tools, we recently developed orthogonally translating and film-like synthetic organelles that allow to create new enzyme functionalities based on spatial separation. We applied this technology to genetic code expansion (GCE) and showed that it is possible to equip eukaryotic cells with multiple orthogonal genetic codes that enable the specific reprogramming of distinct translational machineries, each with single-residue precision.In this protocol, we describe how synthetic organelles can be used to perform mRNA selective GCE and how they can be further developed to allow the simultaneous incorporation of distinct noncanonical amino acids (ncAAs) into selected proteins and how this can be used to label proteins selectively with fluorescent dyes via bioorthogonal chemistry.

Decoding molecular plasticity of the dark proteome

The mechanisms by which intrinsically disordered proteins (IDPs) engage in rapid and highly selective binding is a subject of considerable interest and represents a central paradigm to nuclear pore complex (NPC) function. Nuclear transport receptors (NTRs) can move through the central channel of the NPC which is filled with hundreds of phenylalanine‐glycine‐rich nucleoporins (FG‐Nups) reaching millimolar concentrations with elusive conformational plasticity. Since site‐specific labeling of proteins with small but highly photostable fluorescent dyes inside cells remains the major bottleneck for directly studying protein dynamics in the cellular interior, we have now developed a semi‐synthetic strategy based on novel artificial amino acids that are easily and site‐specifically introduced into any protein by the natural machinery of the living cell via a newly developed thin‐film synthetic organelle that equips the living cell with up to three genetic codes. This allowed us to develop an experimental approach combining site‐specific fluorescent labeling of IDPs in non‐fixed cells with fluorescent lifetime imaging microscopy (FLIM) to directly decipher the plasticity of FG‐Nups via FRET. Our study enabled a conformational look on the condensated IDPs in the sub‐resolution (roughly (50 nm)3 small cavity) cavity of the NPC. By measuring the end‐to‐end distances of different segments of the labeled FG‐Nups using FLIM‐FRET, we can extract the scaling exponent, which directly describes the conformations of FG‐Nups at their functional status as well as the solvent quality in the cellular and even inner NPC environment.Reinkemeier CD, Lemke EA. Dual film‐like organelles enable spatial separation of orthogonal eukaryotic translation. Cell. 2021 Sep 16;184(19):4886‐4903.e21Celetti G, Paci G, Caria J, VanDelinder V, Bachand G, Lemke EA. The liquid state of FG‐nucleoporins mimics permeability barrier properties of nuclear pore complexes. J Cell Bio. (2020) Jan 6;219(1).Reinkemeier CD, Estrada Girona G, Lemke EA, 2019 Designer membraneless organelles enable codon reassignment of selected mRNAs in eukaryotes. Science, Mar 29;363(6434)Nikić I, Estrada Girona G, Kang JH, Paci G, rei S, Koehler C, Shymanska NV, Ventura Santos C, Spitz D, Lemke EA, Debugging Eukaryotic Genetic Code Expansion for Site‐Specific Click‐PAINT Super‐Resolution Microscopy. Angew Chem Int Ed Engl. (2016) Dec 23;55(52):16172‐16176

Pore structure controls stability and molecular flux in engineered protein cages.

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.

Condensed, Microtubule-coating Thin Organelles for Orthogonal Translation in Mammalian Cells

Membraneless organelles are capable of selectively performing complex tasks in living cells despite dynamically exchanging with their surroundings. This is an exquisite example how self-organization of proteins and RNAs can lead to more complex functionalities in living systems. Importantly, the absence of a membrane boundary can enable easier access to larger macromolecular complexes that can be challenging to be transported across a membrane. We previously formed orthogonally translating designer membraneless organelles by combining phase separation with kinesin motor proteins to highly enrich engineered translational factors in large organelles. We also showed that even submicron thick designer organelles can be formed, by mounting them onto membranes, which, presumable assisted by 2D condensation, leads to thin film-like condensates. In this study we show that orthogonal translation can also be built with fiber-like appearing organelles. Here, the microtubule-end binding protein EB1 was used to form fiber-like OT organelles along the microtubule cytoskeleton that perform highly selective and efficient orthogonal translation. We also show an improved simplified design of OT organelles. Together this extends OT organelle technology and demonstrates that the microtubule cytoskeleton is a powerful platform for advanced synthetic organelle engineering.

Synthetic Silica Nano‐Organelles for Regulation of Cascade Reactions in Multi‐Compartmentalized Systems

AbstractIn eukaryotic cells, enzymes are compartmentalized into specific organelles so that different reactions and processes can be performed efficiently and with a high degree of control. In this work, we show that these features can be artificially emulated in robust synthetic organelles constructed using an enzyme co‐compartmentalization strategy. We describe an in situ encapsulation approach that allows enzymes to be loaded into silica nanoreactors in well‐defined compositions. The nanoreactors can be combined into integrated systems to produce a desired reaction outcome. We used the selective enzyme co‐compartmentalization and nanoreactor integration to regulate competitive cascade reactions and to modulate the kinetics of sequential reactions involving multiple nanoreactors. Furthermore, we show that the nanoreactors can be efficiently loaded into giant polymer vesicles, resulting in multi‐compartmentalized microreactors.

Synthetic Silica Nano-Organelles for Regulation of Cascade Reactions in Multi-Compartmentalized Systems.

In eukaryotic cells, enzymes are compartmentalized into specific organelles so that different reactions and processes can be performed efficiently and with a high degree of control. In this work, we show that these features can be artificially emulated in robust synthetic organelles constructed using an enzyme co‐compartmentalization strategy. We describe an in situ encapsulation approach that allows enzymes to be loaded into silica nanoreactors in well‐defined compositions. The nanoreactors can be combined into integrated systems to produce a desired reaction outcome. We used the selective enzyme co‐compartmentalization and nanoreactor integration to regulate competitive cascade reactions and to modulate the kinetics of sequential reactions involving multiple nanoreactors. Furthermore, we show that the nanoreactors can be efficiently loaded into giant polymer vesicles, resulting in multi‐compartmentalized microreactors.

Morphological and functional characteristics of satellite glial cells in the peripheral nervous system.

Satellite glial cells are specialised cells that form a functional perineuronal sheath around sensory ganglion neurons. There are a large number of studies that reveal the morphological and functional characteristics of these cells. Satellite glial cells have been studied both in intact ganglions and in tissue cultures, using light and transmission electron microscopy, immunohistochemical and other methods. Satellite glial cells have polygonal form; they are mononuclear and have developed synthetic organelles, numerous receptors, adhesion molecules and ion channels, which enable them to interact with adjacent neurons, as well as transmit signals in the ganglions of the peripheral nervous system. Based on the literature data, satellite glial cells thanks to their characteristics can receive signals from other cells and react to changes in their surroundings. Previous studies have investigated the potential role of satellite glial cells in the formation of the blood-nervous tissue barrier of the peripheral nervous system, as well as in the neuropathic pain genesis. Some recent discoveries support the fact that satellite glial cells can participate in controlling of local viral infections and protecting pseudounipolar neurons from mentioned infections.

Dual film-like organelles enable spatial separation of orthogonal eukaryotic translation

SummaryEngineering new functionality into living eukaryotic systems by enzyme evolution or de novo protein design is a formidable challenge. Cells do not rely exclusively on DNA-based evolution to generate new functionality but often utilize membrane encapsulation or formation of membraneless organelles to separate distinct molecular processes that execute complex operations. Applying this principle and the concept of two-dimensional phase separation, we develop film-like synthetic organelles that support protein translation on the surfaces of various cellular membranes. These sub-resolution synthetic films provide a path to make functionally distinct enzymes within the same cell. We use these film-like organelles to equip eukaryotic cells with dual orthogonal expanded genetic codes that enable the specific reprogramming of distinct translational machineries with single-residue precision. The ability to spatially tune the output of translation within tens of nanometers is not only important for synthetic biology but has implications for understanding the function of membrane-associated protein condensation in cells.