Toward synthetic life: Biomimetic synthetic cell communication

Living cells and biological mechanisms as prototypes for developing chemical artificial intelligence

Artificial Intelligence (AI) is having a revolutionary impact on our societies. It is helping humans in facing the global challenges of this century. Traditionally, AI is developed in software or through neuromorphic engineering in hardware. More recently, a brand-new strategy has been proposed. It is the so-called Chemical AI (CAI), which exploits molecular, supramolecular, and systems chemistry in wetware to mimic human intelligence. In this work, two promising approaches for boosting CAI are described. One regards designing and implementing neural surrogates that can communicate through optical or chemical signals and give rise to networks for computational purposes and to develop micro/nanorobotics. The other approach concerns "bottom-up synthetic cells" that can be exploited for applications in various scenarios, including future nano-medicine. Both topics are presented at a basic level, mainly to inform the broader audience of non-specialists, and so favour the rise of interest in these frontier subjects.

Chemomechanical Communication between Liposomes Based on Enzyme Cascades

Communication between cells is crucial to the survival of both uni- and multicellular organisms. The primary mode of communication involves chemical cues. There is great current interest in mimicking this behavior in synthetic cells to understand the physical basis of intercellular communication and design collective functional behavior. Using liposomal cell mimics, we demonstrate how a chemical input can elicit a mechanical response (enhanced motility). We employed a single substrate to trigger enzyme cascade-induced control of the diffusion of up to three different liposome populations. Furthermore, substrate competition allows temporal control over enhanced diffusion. The use of enzyme cascades to propagate chemical signals provides a robust and efficient mechanism for diverse populations of protocells to coordinate their motion in response to signals from each other.

Building Synthetic Cells─From the Technology Infrastructure to Cellular Entities

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.

Artificial cell synthesis using biocatalytic polymerization-induced self-assembly

Artificial cells are biomimetic microstructures that mimic functions of natural cells, can be applied as building blocks for molecular systems engineering, and host synthetic biology pathways. Here we report enzymatically synthesized polymer-based artificial cells with the ability to express proteins. Artificial cells were synthesized using biocatalytic atom transfer radical polymerization-induced self-assembly, in which myoglobin synthesizes amphiphilic block co-polymers that self-assemble into structures such as micelles, worm-like micelles, polymersomes and giant unilamellar vesicles (GUVs). The GUVs encapsulate cargo during the polymerization, including enzymes, nanoparticles, microparticles, plasmids and cell lysate. The resulting artificial cells act as microreactors for enzymatic reactions and for osteoblast-inspired biomineralization. Moreover, they can express proteins such as a fluorescent protein and actin when fed with amino acids. Actin polymerizes in the vesicles and alters the artificial cells' internal structure by creating internal compartments. Thus, biocatalytic atom transfer radical polymerization-induced self-assembly-derived GUVs can mimic bacteria as they are composed of a microscopic reaction compartment that contains genetic information for protein expression upon induction.

Controlled exchange of protein and nucleic acid signals from and between synthetic minimal cells

Synthetic minimal cells are a class of bioreactors that have some, but not all, functions of live cells. Here, we report a critical step toward the development of a bottom-up minimal cell: cellular export of functional protein and RNA products. We used cell-penetrating peptide tags to translocate payloads across a synthetic cell vesicle membrane. We demonstrated efficient transport of active enzymes and transport of nucleic acid payloads by RNA-binding proteins. We investigated influence of a concentration gradient alongside other factors on the efficiency of the translocation, and we show a method to increase product accumulation in one location. We demonstrate the use of this technology to engineer molecular communication between different populations of synthetic cells, to exchange protein and nucleic acid signals. The synthetic minimal cell production and export of proteins or nucleic acids allows experimental designs that approach the complexity and relevancy of natural biological systems. A record of this paper's transparent peer review process is included in the supplemental information.

Advancing Biomimetic Functions of Synthetic Cells through Compartmentalized Cell-Free Protein Synthesis

Synthetic cells are artificial constructs that mimic the structures and functions of living cells. They are attractive for studying diverse biochemical processes and elucidating the origins of life. While creating a living synthetic cell remains a grand challenge, researchers have successfully synthesized hundreds of unique synthetic cell platforms. One promising approach to developing more sophisticated synthetic cells is to integrate cell-free protein synthesis (CFPS) mechanisms into vesicle platforms. This makes it possible to create synthetic cells with complex biomimetic functions such as genetic circuits, autonomous membrane modifications, sensing and communication, and artificial organelles. This Review explores recent advances in the use of CFPS to impart advanced biomimetic structures and functions to bottom-up synthetic cell platforms. We also discuss the potential applications of synthetic cells in biomedicine as well as the future directions of synthetic cell research.

Evolution and synthetic biology

Evolutionary observations have often served as an inspiration for biological design. Decoding of the central dogma of life at a molecular level and understanding of the cellular biochemistry have been elegantly used to engineer various synthetic biology applications, including building genetic circuits in vitro and in cells, building synthetic translational systems, and metabolic engineering in cells to biosynthesize and even bioproduce complex high-value molecules. Here, we review three broad areas of synthetic biology that are inspired by evolutionary observations: (i) combinatorial approaches toward cell-based biomolecular evolution, (ii) engineering interdependencies to establish microbial consortia, and (iii) synthetic immunology. In each of the areas, we will highlight the evolutionary premise that was central toward designing these platforms. These are only a subset of the examples where evolution and natural phenomena directly or indirectly serve as a powerful source of inspiration in shaping synthetic biology and biotechnology.

Rapid Generation of Therapeutic Nanoparticles Using Cell-Free Expression Systems

The surface modification of membrane-based nanoparticles, such as liposomes, polymersomes, and lipid nanoparticles, with targeting molecules, such as binding proteins, is an important step in the design of therapeutic materials. However, this modification can be costly and time-consuming, requiring cellular hosts for protein expression and lengthy purification and conjugation steps to attach proteins to the surface of nanocarriers, which ultimately limits the development of effective protein-conjugated nanocarriers. Here, the use of cell-free protein synthesis systems to rapidly create protein-conjugated membrane-based nanocarriers is demonstrated. Using this approach, multiple types of functional binding proteins, including affibodies, computationally designed proteins, and scFvs, can be cell-free expressed and conjugated to liposomes in one-pot. The technique can be expanded further to other nanoparticles, including polymersomes and lipid nanoparticles, and is amenable to multiple conjugation strategies, including surface attachment to and integration into nanoparticle membranes. Leveraging these methods, rapid design of bispecific artificial antigen presenting cells and enhanced delivery of lipid nanoparticle cargo in vitro is demonstrated. It is envisioned that this workflow will enable the rapid generation of membrane-based delivery systems and bolster our ability to create cell-mimetic therapeutics.

Toward Artificial Cell-Mediated Tissue Engineering: A New Perspective

The fast-growing pace of regenerative medicine research has allowed the development of a range of novel approaches to tissue engineering applications. Until recently, the main points of interest in the majority of studies have been to combine different materials to control cellular behavior and use different techniques to optimize tissue formation, from 3-D bioprinting to in situ regeneration. However, with the increase of the understanding of the fundamentals of cellular organization, tissue development, and regeneration, has also come the realization that for the next step in tissue engineering, a higher level of spatiotemporal control on cell-matrix interactions is required. It is proposed that the combination of artificial cell research with tissue engineering could provide a route toward control over complex tissue development. By equipping artificial cells with the underlying mechanisms of cellular functions, such as communication mechanisms, migration behavior, or the coherent behavior of cells depending on the surrounding matrix properties, they can be applied in instructing native cells into desired differentiation behavior at a resolution not to be attained with traditional matrix materials.

Exploring Giant Unilamellar Vesicle Production for Artificial Cells - Current Challenges and Future Directions

Creating an artificial cell from the bottom up is a long-standing challenge and, while significant progress has been made, the full realization of this goal remains elusive. Arguably, one of the biggest hurdles that researchers are facing now is the assembly of different modules of cell function inside a single container. Giant unilamellar vesicles (GUVs) have emerged as a suitable container with many methods available for their production. Well-studied swelling-based methods offer a wide range of lipid compositions but at the expense of limited encapsulation efficiency. Emulsion-based methods, on the other hand, excel at encapsulation but are only effective with a limited set of membrane compositions and may entrap residual additives in the lipid bilayer. Since the ultimate artificial cell will need to comply with both specific membrane and encapsulation requirements, there is still no one-method-fits-all solution for GUV formation available today. This review discusses the state of the art in different GUV production methods and their compatibility with GUV requirements and operational requirements such as reproducibility and ease of use. It concludes by identifying the most pressing issues and proposes potential avenues for future research to bring us one step closer to turning artificial cells into a reality.

On biochemical constructors and synthetic cells

Is it possible to build life? More specifically, is it possible to create a living synthetic cell from inanimate building blocks? This question precipitated into one of the most significant grand challenges in biochemistry and synthetic biology, with several large research consortia forming around this endeavour in Europe (European Synthetic Cell Initiative), the USA (Build-a-Cell Initiative) and Japan (Japanese Society for Cell Synthesis Research). The mature field of biochemistry, the advent of synthetic biology in the early 2000s, and the burgeoning field of cell-free synthetic biology made it feasible to tackle this grand challenge.

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.

A Synthetic Signaling Network Imitating the Action of Immune Cells in Response to Bacterial Metabolism

State-of-the-art bottom-up synthetic biology allows to replicate many basic biological functions in artificial-cell-like devices. To mimic more complex behaviors, however, artificial cells would need to perform many of these functions in a synergistic and coordinated fashion, which remains elusive. Here, a sophisticated biological response is considered, namely the capture and deactivation of pathogens by neutrophil immune cells, through the process of netosis. A consortium consisting of two synthetic agents is designed-responsive DNA-based particles and antibiotic-loaded lipid vesicles-whose coordinated action mimics the sought immune-like response when triggered by bacterial metabolism. The artificial netosis-like response emerges from a series of interlinked sensing and communication pathways between the live and synthetic agents, and translates into both physical and chemical antimicrobial actions, namely bacteria immobilization and exposure to antibiotics. The results demonstrate how advanced life-like responses can be prescribed with a relatively small number of synthetic molecular components, and outlines a new strategy for artificial-cell-based antimicrobial solutions.

The Expanded Central Dogma: Genome Resynthesis, Orthogonal Biosystems, Synthetic Genetics

Synthetic biology seeks to probe fundamental aspects of biological form and function by construction [i.e., (re)synthesis] rather than deconstruction (analysis). In this sense, biological sciences now follow the lead given by the chemical sciences. Synthesis can complement analytic studies but also allows novel approaches to answering fundamental biological questions and opens up vast opportunities for the exploitation of biological processes to provide solutions for global problems. In this review, we explore aspects of this synthesis paradigm as applied to the chemistry and function of nucleic acids in biological systems and beyond, specifically, in genome resynthesis, synthetic genetics (i.e., the expansion of the genetic alphabet, of the genetic code, and of the chemical make-up of genetic systems), and the elaboration of orthogonal biosystems and components.

Molecular and cellular level characterization of cytoskeletal mechanics using a quartz crystal microbalance

A quartz crystal microbalance (QCM) is an instrument that has the ability to measure nanogram-level changes in mass on a quartz sensor and is traditionally used to probe surface interactions and assembly kinetics of synthetic systems. The addition of dissipation monitoring (QCM-D) facilitates the study of viscoelastic systems, such as those relevant to molecular and cellular mechanics. Due to real-time recording of frequency and dissipation changes and single protein-level precision, the QCM-D is effective in interrogating the viscoelastic properties of cell surfaces and in vitro cellular components. However, few studies focus on the application of this instrument to cytoskeletal systems, whose dynamic parts create interesting emergent mechanics as ensembles that drive essential tasks, such as division and motility. Here, we review the ability of the QCM-D to characterize key kinetic and mechanical features of the cytoskeleton through in vitro reconstitution and cellular assays and outline how QCM-D studies can yield insightful mechanical data alone and in tandem with other biophysical characterization techniques.

Minimal Out-of-Equilibrium Metabolism for Synthetic Cells: A Membrane Perspective

Life-like systems need to maintain a basal metabolism, which includes importing a variety of building blocks required for macromolecule synthesis, exporting dead-end products, and recycling cofactors and metabolic intermediates, while maintaining steady internal physical and chemical conditions (physicochemical homeostasis). A compartment, such as a unilamellar vesicle, functionalized with membrane-embedded transport proteins and metabolic enzymes encapsulated in the lumen meets these requirements. Here, we identify four modules designed for a minimal metabolism in a synthetic cell with a lipid bilayer boundary: energy provision and conversion, physicochemical homeostasis, metabolite transport, and membrane expansion. We review design strategies that can be used to fulfill these functions with a focus on the lipid and membrane protein composition of a cell. We compare our bottom-up design with the equivalent essential modules of JCVI-syn3a, a top-down genome-minimized living cell with a size comparable to that of large unilamellar vesicles. Finally, we discuss the bottlenecks related to the insertion of a complex mixture of membrane proteins into lipid bilayers and provide a semiquantitative estimate of the relative surface area and lipid-to-protein mass ratios (i.e., the minimal number of membrane proteins) that are required for the construction of a synthetic cell.

Polymerization-Induced Proteinosome Formation Initiated by Artificial Cells

Cellular communication is essential for living cells to coordinate the individual cellular responses and make collective behaviors. In the past decade, the communications between artificial cells have aroused great interest due to the potential applications of the structures in bioscience and biotechnology. To mimic the cellular communication, artificial cell assisted synthesis of proteinosomes was studied in this research. Multienzyme proteinosomes with glucose oxidase (GOx) and horseradish peroxidase (HRP) decorated on the membranes were synthesized by the thermally triggered self-assembly approach. Free radicals produced in a cascade reaction taking place on the surfaces of the multienzyme proteinosomes initiated reversible addition-fragmentation chain transfer (RAFT) polymerization of NIPAM at a temperature above LCST of PNIPAM in the presence of bovine serum albumin (BSA) or alcohol dehydrogenase (ADH)/acetaldehyde dehydrogenase (ALDH), and daughter proteinosomes with BSA or ADH/ALDH on the surfaces were fabricated. The structures of the GOx/HRP initiator proteinosomes, and the synthesized daughter proteinosomes were characterized with transmission electron microscopy, atomic force microscopy, fluorescence microscopy, dynamic light scattering, and micro-DSC. Enzyme activity assays demonstrate the high bioactivities of the enzymes on the surfaces of the initiator and the synthesized daughter proteinosomes.

Engineering Cyborg Bacteria Through Intracellular Hydrogelation

Natural and artificial cells are two common chassis in synthetic biology. Natural cells can perform complex tasks through synthetic genetic constructs, but their autonomous replication often causes safety concerns for biomedical applications. In contrast, artificial cells based on nonreplicating materials, albeit possessing reduced biochemical complexity, provide more defined and controllable functions. Here, for the first time, the authors create hybrid material-cell entities termed Cyborg Cells. To create Cyborg Cells, a synthetic polymer network is assembled inside each bacterium, rendering them incapable of dividing. Cyborg Cells preserve essential functions, including cellular metabolism, motility, protein synthesis, and compatibility with genetic circuits. Cyborg Cells also acquire new abilities to resist stressors that otherwise kill natural cells. Finally, the authors demonstrate the therapeutic potential by showing invasion into cancer cells. This work establishes a new paradigm in cellular bioengineering by exploiting a combination of intracellular man-made polymers and their interaction with the protein networks of living cells.

Parasites, Infections, and Inoculation in Synthetic Minimal Cells

Synthetic minimal cells provide a controllable and engineerable model for biological processes. While much simpler than any live natural cell, synthetic cells offer a chassis for investigating the chemical foundations of key biological processes. Herein, we show a synthetic cell system with host cells, interacting with parasites and undergoing infections of varying severity. We demonstrate how the host can be engineered to resist infection, we investigate the metabolic cost of carrying resistance, and we show an inoculation that immunizes the host against pathogens. Our work expands the synthetic cell engineering toolbox by demonstrating host-pathogen interactions and mechanisms for acquiring immunity. This brings synthetic cell systems one step closer to providing a comprehensive model of complex, natural life.

Light-Activated Assembly of Connexon Nanopores in Synthetic Cells

During developmental processes and wound healing, activation of living cells occurs with spatiotemporal precision and leads to rapid release of soluble molecular signals, allowing communication and coordination between neighbors. Nonliving systems capable of similar responsive release hold great promise for information transfer in materials and site-specific drug delivery. One nonliving system that offers a tunable platform for programming release is synthetic cells. Encased in a lipid bilayer structure, synthetic cells can be outfitted with molecular conduits that span the bilayer and lead to material exchange. While previous work expressing membrane pore proteins in synthetic cells demonstrated content exchange, user-defined control over release has remained elusive. In mammalian cells, connexon nanopore structures drive content release and have garnered significant interest since they can direct material exchange through intercellular contacts. Here, we focus on connexon nanopores and present activated release of material from synthetic cells in a light-sensitive fashion. To do this, we re-engineer connexon nanopores to assemble after post-translational processing by a protease. By encapsulating proteases in light-sensitive liposomes, we show that assembly of nanopores can be triggered by illumination, resulting in rapid release of molecules encapsulated within synthetic cells. Controlling connexon nanopore activity provides an opportunity for initiating communication with extracellular signals and for transferring molecular agents to the cytoplasm of living cells in a rapid, light-guided manner.

Toward Interdisciplinary Synergies in Molecular Communications: Perspectives from Synthetic Biology, Nanotechnology, Communications Engineering and Philosophy of Science

Within many chemical and biological systems, both synthetic and natural, communication via chemical messengers is widely viewed as a key feature. Often known as molecular communication, such communication has been a concern in the fields of synthetic biologists, nanotechnologists, communications engineers, and philosophers of science. However, interactions between these fields are currently limited. Nevertheless, the fact that the same basic phenomenon is studied by all of these fields raises the question of whether there are unexploited interdisciplinary synergies. In this paper, we summarize the perspectives of each field on molecular communications, highlight potential synergies, discuss ongoing challenges to exploit these synergies, and present future perspectives for interdisciplinary efforts in this area.

Artificial cell design: reconstructing biology for life science applications

Artificial cells are developed to redesign novel biological functions in a programmable and tunable manner. Although it aims to reconstitute living cell features and address 'origin of life' related questions, rapid development over the years has transformed artificial cells into an engineering tool with huge potential in applied biotechnology. Although the application of artificial cells was introduced decades ago as drug carriers, applications in other sectors are relatively new and could become possible with the technological advancement that can modulate its designing principles. Artificial cells are non-living system that includes no prerequisite designing modules for their formation and therefore allow freedom of assembling desired biological machinery within a physical boundary devoid of complex contemporary living-cell counterparts. As stimuli-responsive biomimetic tools, artificial cells are programmed to sense the surrounding, recognise their target, activate its function and perform the defined task. With the advantage of their customised design, artificial cells are being studied in biosensing, drug delivery, anti-cancer therapeutics or artificial photosynthesis type fields. This mini-review highlights those advanced fields where artificial cells with a minimalistic setup are developed as user-defined custom-made microreactors, targeting to reshape our future 'life'.

Actinosomes: Condensate-Templated Containers for Engineering Synthetic Cells

Engineering synthetic cells has a broad appeal, from understanding living cells to designing novel biomaterials for therapeutics, biosensing, and hybrid interfaces. A key prerequisite to creating synthetic cells is a three-dimensional container capable of orchestrating biochemical reactions. In this study, we present an easy and effective technique to make cell-sized porous containers, coined actinosomes, using the interactions between biomolecular condensates and the actin cytoskeleton. This approach uses polypeptide/nucleoside triphosphate condensates and localizes actin monomers on their surface. By triggering actin polymerization and using osmotic gradients, the condensates are transformed into containers, with the boundary made up of actin filaments and polylysine polymers. We show that the guanosine triphosphate (GTP)-to-adenosine triphosphate (ATP) ratio is a crucial parameter for forming actinosomes: insufficient ATP prevents condensate dissolution, while excess ATP leads to undesired crumpling. Permeability studies reveal the porous surface of actinosomes, allowing small molecules to pass through while restricting bigger macromolecules within the interior. We show the functionality of actinosomes as bioreactors by carrying out in vitro protein translation within them. Actinosomes are a handy addition to the synthetic cell platform, with appealing properties like ease of production, inherent encapsulation capacity, and a potentially active surface to trigger signaling cascades and form multicellular assemblies, conceivably useful for biotechnological applications.

Hydrogels as functional components in artificial cell systems

Recent years have seen substantial efforts aimed at constructing artificial cells from various molecular components with the aim of mimicking the processes, behaviours and architectures found in biological systems. Artificial cell development ultimately aims to produce model constructs that progress our understanding of biology, as well as forming the basis for functional bio-inspired devices that can be used in fields such as therapeutic delivery, biosensing, cell therapy and bioremediation. Typically, artificial cells rely on a bilayer membrane chassis and have fluid aqueous interiors to mimic biological cells. However, a desire to more accurately replicate the gel-like properties of intracellular and extracellular biological environments has driven increasing efforts to build cell mimics based on hydrogels. This has enabled researchers to exploit some of the unique functional properties of hydrogels that have seen them deployed in fields such as tissue engineering, biomaterials and drug delivery. In this Review, we explore how hydrogels can be leveraged in the context of artificial cell development. We also discuss how hydrogels can potentially be incorporated within the next generation of artificial cells to engineer improved biological mimics and functional microsystems.

Controlling Synthetic Cell-Cell Communication

Synthetic cells, which mimic cellular function within a minimal compartment, are finding wide application, for instance in studying cellular communication and as delivery devices to living cells. However, to fully realise the potential of synthetic cells, control of their function is vital. An array of tools has already been developed to control the communication of synthetic cells to neighbouring synthetic cells or living cells. These tools use either chemical inputs, such as small molecules, or physical inputs, such as light. Here, we examine these current methods of controlling synthetic cell communication and consider alternative mechanisms for future use.