Multiscale remodeling of biomembranes and vesicles

Biomembranes and vesicles cover a wide range of length scales. Indeed, small nanovesicles have a diameter of a few tens of nanometers whereas giant vesicles can have diameters up to hundreds of micrometers. The remodeling of giant vesicles on the micron scale can be observed by light microscopy and understood by the theory of curvature elasticity, which represents a top-down approach. The theory predicts the formation of multispherical shapes as recently observed experimentally. On the nanometer scale, much insight has been obtained via coarse-grained molecular dynamics simulations of nanovesicles, which provides a bottom-up approach based on the lipid numbers assembled in the two bilayer leaflets and the resulting leaflet tensions. The remodeling processes discussed here include the shape transformations of vesicles, their morphological responses to the adhesion of condensate droplets, the instabilities of lipid bilayers and nanovesicles, as well as the topological transformations of vesicles by membrane fission and fusion. The latter processes determine the complex topology of the endoplasmic reticulum.

Photoactivation of LOV domains with chemiluminescence

Optogenetics has opened new possibilities in the remote control of diverse cellular functions with high spatiotemporal precision using light. However, delivering light to optically non-transparent systems remains a challenge. Here, we describe the photoactivation of light-oxygen-voltage-sensing domains (LOV domains) with in situ generated light from a chemiluminescence reaction between luminol and H2O2. This activation is possible due to the spectral overlap between the blue chemiluminescence emission and the absorption bands of the flavin chromophore in LOV domains. All four LOV domain proteins with diverse backgrounds and structures (iLID, BcLOV4, nMagHigh/pMagHigh, and VVDHigh) were photoactivated by chemiluminescence as demonstrated using a bead aggregation assay. The photoactivation with chemiluminescence required a critical light-output below which the LOV domains reversed back to their dark state with protein characteristic kinetics. Furthermore, spatially confined chemiluminescence produced inside giant unilamellar vesicles (GUVs) was able to photoactivate proteins both on the membrane and in solution, leading to the recruitment of the corresponding proteins to the GUV membrane. Finally, we showed that reactive oxygen species produced by neutrophil like cells can be converted into sufficient chemiluminescence to recruit the photoswitchable protein BcLOV4-mCherry from solution to the cell membrane. The findings highlight the utility of chemiluminescence as an endogenous light source for optogenetic applications, offering new possibilities for studying cellular processes in optically non-transparent systems.

Hierarchical Structuration in Protocellular System

Spatial control is one of the ubiquitous features in biological systems and the key to the functional complexity of living cells. The strategies to achieve such precise spatial control in protocellular systems are crucial to constructing complex artificial living systems with functional collective behavior. Herein, the authors review recent advances in the spatial control within a single protocell or between different protocells and discuss how such hierarchical structured protocellular system can be used to understand complex living systems or to advance the development of functional microreactors with the programmable release of various biomacromolecular payloads, or smart protocell-biological cell hybrid system.

Dimerization of iLID optogenetic proteins observed using 3D single-molecule tracking in live E. coli

3D single-molecule tracking microscopy has enabled measurements of protein diffusion in living cells, offering information about protein dynamics and cellular environments. For example, different diffusive states can be resolved and assigned to protein complexes of different size and composition. However, substantial statistical power and biological validation, often through genetic deletion of binding partners, are required to support diffusive state assignments. When investigating cellular processes, real-time perturbations to protein spatial distributions is preferable to permanent genetic deletion of an essential protein. For example, optogenetic dimerization systems can be used to manipulate protein spatial distributions that could offer a means to deplete specific diffusive states observed in single-molecule tracking experiments. Here, we evaluate the performance of the iLID optogenetic system in living E. coli cells using diffraction-limited microscopy and 3D single-molecule tracking. We observed a robust optogenetic response in protein spatial distributions after 488 nm laser activation. Surprisingly, 3D single-molecule tracking results indicate activation of the optogenetic response when illuminating with high-intensity light with wavelengths at which there is minimal photon absorbance by the LOV2 domain. The preactivation can be minimized through the use of iLID system mutants, and titration of protein expression levels.

Self-Regulated and Bidirectional Communication in Synthetic Cell Communities

Cell-to-cell communication is not limited to a sender releasing a signaling molecule and a receiver perceiving it but is often self-regulated and bidirectional. Yet, in communities of synthetic cells, such features that render communication efficient and adaptive are missing. Here, we report the design and implementation of adaptive two-way signaling with lipid-vesicle-based synthetic cells. The first layer of self-regulation derives from coupling the temporal dynamics of the signal, H2O2, production in the sender to adhesions between sender and receiver cells. This way the receiver stays within the signaling range for the duration sender produces the signal and detaches once the signal fades. Specifically, H2O2 acts as both a forward signal and a regulator of the adhesions by activating photoswitchable proteins at the surface for the duration of the chemiluminescence. The second layer of self-regulation arises when the adhesions render the receiver permeable and trigger the release of a backward signal, resulting in bidirectional exchange. These design rules provide a concept for engineering multicellular systems with adaptive communication.

A disordered tether to iLID improves photoswitchable protein patterning on model membranes

Reversible protein patterning on model membranes is important to reproduce spatiotemporal protein dynamics in vitro. An engineered version of iLID, disiLID, with a disordered domain as a membrane tether improves the recruitment of Nano under blue light and the reversibility in the dark, which enables protein patterning on membranes with higher spatiotemporal precision.

Hedgehog is relayed through dynamic heparan sulfate interactions to shape its gradient

Cellular differentiation is directly determined by concentration gradients of morphogens. As a central model for gradient formation during development, Hedgehog (Hh) morphogens spread away from their source to direct growth and pattern formation in Drosophila wing and eye discs. What is not known is how extracellular Hh spread is achieved and how it translates into precise gradients. Here we show that two separate binding areas located on opposite sides of the Hh molecule can interact directly and simultaneously with two heparan sulfate (HS) chains to temporarily cross-link the chains. Mutated Hh lacking one fully functional binding site still binds HS but shows reduced HS cross-linking. This, in turn, impairs Hhs ability to switch between both chains in vitro and results in striking Hh gradient hypomorphs in vivo. The speed and propensity of direct Hh switching between HS therefore shapes the Hh gradient, revealing a scalable design principle in morphogen-patterned tissues.

Drosophila hedgehog signaling range and robustness depend on direct and sustained heparan sulfate interactions

Morphogens determine cellular differentiation in many developing tissues in a concentration dependent manner. As a central model for gradient formation during animal development, Hedgehog (Hh) morphogens spread away from their source to direct growth and pattern formation in the Drosophila wing disc. Although heparan sulfate (HS) expression in the disc is essential for this process, it is not known whether HS regulates Hh signaling and spread in a direct or in an indirect manner. To answer this question, we systematically screened two composite Hh binding areas for HS in vitro and expressed mutated proteins in the Drosophila wing disc. We found that selectively impaired HS binding of the second site reduced Hh signaling close to the source and caused striking wing mispatterning phenotypes more distant from the source. These observations suggest that HS constrains Hh to the wing disc epithelium in a direct manner, and that interfering with this constriction converts Hh into freely diffusing forms with altered signaling ranges and impaired gradient robustness.

Computational framework for single-cell spatiotemporal dynamics of optogenetic membrane recruitment

We describe a modular computational framework for analyzing cell-wide spatiotemporal signaling dynamics in single-cell microscopy experiments that accounts for the experiment-specific geometric and diffractive complexities that arise from heterogeneous cell morphologies and optical instrumentation. Inputs are unique cell geometries and protein concentrations derived from confocal stacks and spatiotemporally varying environmental stimuli. After simulating the system with a model of choice, the output is convolved with the microscope point-spread function for direct comparison with the observable image. We experimentally validate this approach in single cells with BcLOV4, an optogenetic membrane recruitment system for versatile control over cell signaling, using a three-dimensional non-linear finite element model with all parameters experimentally derived. The simulations recapitulate observed subcellular and cell-to-cell variability in BcLOV4 signaling, allowing for inter-experimental differences of cellular and instrumentation origins to be elucidated and resolved for improved interpretive robustness. This single-cell approach will enhance optogenetics and spatiotemporally resolved signaling studies.

Protocells: Milestones and Recent Advances

The origin of life is still one of humankind's great mysteries. At the transition between nonliving and living matter, protocells, initially featureless aggregates of abiotic matter, gain the structure and functions necessary to fulfill the criteria of life. Research addressing protocells as a central element in this transition is diverse and increasingly interdisciplinary. The authors review current protocell concepts and research directions, address milestones, challenges and existing hypotheses in the context of conditions on the early Earth, and provide a concise overview of current protocell research methods.

Synthetic cells with self-activating optogenetic proteins communicate with natural cells

Development of regulated cellular processes and signaling methods in synthetic cells is essential for their integration with living materials. Light is an attractive tool to achieve this, but the limited penetration depth into tissue of visible light restricts its usability for in-vivo applications. Here, we describe the design and implementation of bioluminescent intercellular and intracellular signaling mechanisms in synthetic cells, dismissing the need for an external light source. First, we engineer light generating SCs with an optimized lipid membrane and internal composition, to maximize luciferase expression levels and enable high-intensity emission. Next, we show these cells’ capacity to trigger bioprocesses in natural cells by initiating asexual sporulation of dark-grown mycelial cells of the fungus Trichoderma atroviride. Finally, we demonstrate regulated transcription and membrane recruitment in synthetic cells using bioluminescent intracellular signaling with self-activating fusion proteins. These functionalities pave the way for deploying synthetic cells as embeddable microscale light sources that are capable of controlling engineered processes inside tissues.

Synthetic biology and engineering approaches are harnessed to incorporate new capabilities in synthetic cells. Here, the authors designed bioluminescent signaling mechanisms for intracellular and intercellular synthetic-to-natural cell communication.

Cell to Cell Signaling through Light in Artificial Cell Communities: Glowing Predator Lures Prey

Cells commonly communicate with each other through diffusible molecules but nonchemical communication remains elusive. While bioluminescent organisms communicate through light to find prey or attract mates, it is still under debate if signaling through light is possible at the cellular level. Here, we demonstrate that cell to cell signaling through light is possible in artificial cell communities derived from biomimetic vesicles. In our design, artificial sender cells produce an intracellular light signal, which triggers the adhesion to receiver cells. Unlike soluble molecules, the light signal propagates fast, independent of diffusion and without the need for a transporter across membranes. To obtain a predator-prey relationship, the luminescence predator cells is loaded with a secondary diffusible poison, which is transferred to the prey cell upon adhesion and leads to its lysis. This design provides a blueprint for light based intercellular communication, which can be used for programing artificial and natural cell communities.

Patterning Microtubule Network Organization Reshapes Cell-Like Compartments

Eukaryotic cells contain a cytoskeletal network comprised of dynamic microtubule filaments whose spatial organization is highly plastic. Specialized microtubule architectures are optimized for different cell types and remodel with the oscillatory cell cycle. These spatially distinct microtubule networks are thought to arise from the activity and localization of microtubule regulators and motors and are further shaped by physical forces from the cell boundary. Given complexities and redundancies of a living cell, it is challenging to disentangle the separate biochemical and physical contributions to microtubule network organization. Therefore, we sought to develop a minimal cell-like system to manipulate and spatially pattern the organization of cytoskeletal components in real-time, providing an opportunity to build distinct spatial structures and to determine how they are shaped by or reshape cell boundaries. We constructed a system for induced spatial patterning of protein components within cell-sized emulsion compartments and used it to drive microtubule network organization in real-time. We controlled dynamic protein relocalization using small molecules and light and slowed lateral diffusion within the lipid monolayer to create stable micropatterns with focused illumination. By fusing microtubule interacting proteins to optochemical dimerization domains, we directed the spatial organization of microtubule networks. Cortical patterning of polymerizing microtubules leads to symmetry breaking and forces that dramatically reshape the compartment. Our system has applications in cell biology to characterize the contributions of biochemical components and physical boundary conditions to microtubule network organization. Additionally, active shape control has uses in protocell engineering and for augmenting the functionalities of synthetic cells.

Generation and Characterization of a Polyclonal Human Reference Antibody to Measure Anti-Drug Antibody Titers in Patients with Fabry Disease

Male patients with Fabry disease (FD) are at high risk for the formation of antibodies to recombinant α-galactosidase A (AGAL), used for enzyme replacement therapy. Due to the rapid disease progression, the identification of patients at risk is highly warranted. However, currently suitable references and standardized protocols for anti-drug antibodies (ADA) determination do not exist. Here we generate a comprehensive patient-derived antibody mixture as a reference, allowing ELISA-based quantification of antibody titers from individual blood samples. Serum samples of 22 male patients with FD and ADAs against AGAL were pooled and purified by immune adsorption. ADA-affinities against agalsidase-α, agalsidase-β and Moss-AGAL were measured by quartz crystal microbalance with dissipation monitoring (QCM-D). AGAL-specific immune adsorption generated a polyclonal ADA mixture showing a concentration-dependent binding and inhibition of AGAL. Titers in raw sera and from purified total IgGs (r2 = 0.9063 and r2 = 0.8952, both p < 0.0001) correlated with the individual inhibitory capacities of ADAs. QCM-D measurements demonstrated comparable affinities of the reference antibody for agalsidase-α, agalsidase-β and Moss-AGAL (KD: 1.94 ± 0.11 µM, 2.46 ± 0.21 µM, and 1.33 ± 0.09 µM, respectively). The reference antibody allows the ELISA-based ADA titer determination and quantification of absolute concentrations. Furthermore, ADAs from patients with FD have comparable affinities to agalsidase-α, agalsidase-β and Moss-AGAL.

Effects of Nano-Protein Complexes on Apoptosis of Myocardial Infarction Cells Based on Complex Curve Analysis

Myocardial infarction is one of the common types of coronary heart disease in the clinic. Its morbidity, lethality and disability are high, and it has become a serious threat to human health. At present, it is shown that in the early stage of acute myocardial infarction, myocardial cells are mainly apoptotic, suggesting that effectively blocking myocardial apoptosis in the early stage of myocardial infarction is of great significance for reducing tissue necrosis in the infarcted area. Recent studies have shown that NG nano-protein complexes have a better therapeutic effect on acute myocardial infarction and can inhibit left ventricular remodeling in patients with acute myocardial infarction. However, there are few studies on the effect of NG nano-protein complexes on myocardial cell apoptosis after ischemia. This study used a rat model of acute myocardial infarction to analyze its effect on apoptotic proteins of myocardial cells in rats with acute myocardial infarction in order to provide a certain theoretical basis for its clinical application. In this study, 45 SD rats were randomly divided into a sham operation group, a myocardial infarction group, and a NG nano-protein complex group, with 15 in each group. The sham operation group only underwent thoracotomy, and received normal saline gavage postoperatively; the myocardial infarction group and the NG nano-protein complex group were ligated to the left anterior descending coronary artery of the rat to establish an acute myocardial infarction model, and were performed separately treatment with saline and NG nanoprotein complexes. Finally, we conclude that this nano-protein complex can significantly reduce the expression level of myocardial apoptosis-related proteins in rats with acute myocardial infarction, and is of great significance in inhibiting the apoptosis of acute myocardial infarction cells.

Multistimuli Sensing Adhesion Unit for the Self-Positioning of Minimal Synthetic Cells

Cells have the ability to sense different environmental signals and position themselves accordingly in order to support their survival. Introducing analogous capabilities to the bottom-up assembled minimal synthetic cells is an important step for their autonomy. Here, a minimal synthetic cell which combines a multistimuli sensitive adhesion unit with an energy conversion module is reported, such that it can adhere to places that have the right environmental parameters for ATP production. The multistimuli sensitive adhesion unit senses light, pH, oxidative stress, and the presence of metal ions and can regulate the adhesion of synthetic cells to substrates in response to these stimuli following a chemically coded logic. The adhesion unit is composed of the light and redox responsive protein interaction of iLID and Nano and the pH sensitive and metal ion mediated binding of protein His-tags to Ni²⁺ -NTA complexes. Integration of the adhesion unit with a light to ATP conversion module into one synthetic cell allows it to adhere to places under blue light illumination, non-oxidative conditions, at neutral pH and in the presence of metal ions, which are the right conditions to synthesize ATP. Thus, the multistimuli responsive adhesion unit allows synthetic cells to self-position and execute their functions.

The Importance of Cell-Cell Interaction Dynamics in Bottom-Up Tissue Engineering: Concepts of Colloidal Self-Assembly in the Fabrication of Multicellular Architectures

Building tissue from cells as the basic building block based on principles of self-assembly is a challenging and promising approach. Understanding how far principles of self-assembly and self-sorting known for colloidal particles apply to cells remains unanswered. In this study, we demonstrate that not just controlling the cell-cell interactions but also their dynamics is a crucial factor that determines the formed multicellular structure, using photoswitchable interactions between cells that are activated with blue light and reverse in the dark. Tuning dynamics of the cell-cell interactions by pulsed light activation results in multicellular architectures with different sizes and shapes. When the interactions between cells are dynamic, compact and round multicellular clusters under thermodynamic control form, while otherwise branched and loose aggregates under kinetic control assemble. These structures parallel what is known for colloidal assemblies under reaction- and diffusion-limited cluster aggregation, respectively. Similarly, dynamic interactions between cells are essential for cells to self-sort into distinct groups. Using four different cell types, which expressed two orthogonal cell-cell interaction pairs, the cells sorted into two separate assemblies. Bringing concepts of colloidal self-assembly to bottom-up tissue engineering provides a new theoretical framework and will help in the design of more predictable tissue-like structures.

Controlled division of cell-sized vesicles by low densities of membrane-bound proteins

The proliferation of life on earth is based on the ability of single cells to divide into two daughter cells. During cell division, the plasma membrane undergoes a series of morphological transformations which ultimately lead to membrane fission. Here, we show that analogous remodeling processes can be induced by low densities of proteins bound to the membranes of cell-sized lipid vesicles. Using His-tagged fluorescent proteins, we are able to precisely control the spontaneous curvature of the vesicle membranes. By fine-tuning this curvature, we obtain dumbbell-shaped vesicles with closed membrane necks as well as neck fission and complete vesicle division. Our results demonstrate that the spontaneous curvature generates constriction forces around the membrane necks and that these forces can easily cover the force range found in vivo. Our approach involves only one species of membrane-bound proteins at low densities, thereby providing a simple and extendible module for bottom-up synthetic biology.

Membrane fission of a cell into two daughters is a core ability of cell-based life. Here the authors show that in artificial cells division can be controlled by regulating membrane curvature using low protein density.

Light controlled cell-to-cell adhesion and chemical communication in minimal synthetic cells

Light controlled adhesions between sender and receiver GUVs, used as minimal synthetic cells, photoregulates their spatial proximity and chemical communication.

Light-Guided Motility of a Minimal Synthetic Cell

Cell motility is an important but complex process; as cells move, new adhesions form at the front and adhesions disassemble at the back. To replicate this dynamic and spatiotemporally controlled asymmetry of adhesions and achieve motility in a minimal synthetic cell, we controlled the adhesion of a model giant unilamellar vesicle (GUV) to the substrate with light. For this purpose, we immobilized the proteins iLID and Micro, which interact under blue light and dissociate from each other in the dark, on a substrate and a GUV, respectively. Under blue light, the protein interaction leads to adhesion of the vesicle to the substrate, which is reversible in the dark. The high spatiotemporal control provided by light, allowed partly illuminating the GUV and generating an asymmetry in adhesions. Consequently, the GUV moves into the illuminated area, a process that can be repeated over multiple cycles. Thus, our system reproduces the dynamic spatiotemporal distribution of adhesions and establishes mimetic motility of a synthetic cell.

Light-Induced Printing of Protein Structures on Membranes in Vitro

Reconstituting functional modules of biological systems in vitro is an important yet challenging goal of bottom-up synthetic biology, in particular with respect to their precise spatiotemporal regulation. One of the most desirable external control parameters for the engineering of biological systems is visible light, owing to its specificity and ease of defined application in space and time. Here we engineered the PhyB-PIF6 system to spatiotemporally target proteins by light onto model membranes and thus sequentially guide protein pattern formation and structural assembly in vitro from the bottom up. We show that complex micrometer-sized protein patterns can be printed on time scales of seconds, and the pattern density can be precisely controlled by protein concentration, laser power, and activation time. Moreover, when printing self-assembling proteins such as the bacterial cytoskeleton protein FtsZ, the targeted assembly into filaments and large-scale structures such as artificial rings can be accomplished. Thus, light mediated sequential protein assembly in cell-free systems represents a promising approach to hierarchically building up the next level of complexity toward a minimal cell.

Engineering Proteins at Interfaces: From Complementary Characterization to Material Surfaces with Designed Functions

Once materials come into contact with a biological fluid containing proteins, proteins are generally—whether desired or not—attracted by the material's surface and adsorb onto it. The aim of this Review is to give an overview of the most commonly used characterization methods employed to gain a better understanding of the adsorption processes on either planar or curved surfaces. We continue to illustrate the benefit of combining different methods to different surface geometries of the material. The thus obtained insight ideally paves the way for engineering functional materials that interact with proteins in a predetermined manner.

Reversible Social Self-Sorting of Colloidal Cell-Mimics with Blue Light Switchable Proteins

Toward the bottom-up assembly of synthetic cells from molecular building blocks, it is an ongoing challenge to assemble micrometer sized compartments that host different processes into precise multicompartmental assemblies, also called prototissues. The difficulty lies in controlling interactions between different compartments dynamically both in space and time, as these interactions determine how they organize with respect to each other and how they work together. In this study, we have been able to control the self-assembly and social self-sorting of four different types of colloids, which we use as a model for synthetic cells, into two separate families with visible light. For this purpose we used two photoswitchable protein pairs (iLID/Nano and nHagHigh/pMagHigh) that both reversibly heterodimerize upon blue light exposure and dissociate from each other in the dark. These photoswitchable proteins provide noninvasive, dynamic, and reversible remote control under biocompatible conditions over the self-assembly process with unprecedented spatial and temporal precision. In addition, each protein pair brings together specifically two different types of colloids. The orthogonality of the two protein pairs enables social self-sorting of a four component mixture into two distinct families of colloidal aggregates with controlled arrangements. These results will ultimately pave the way for the bottom-up assembly of multicompartment synthetic prototissues of a higher complexity, enabling us to control precisely and dynamically the organization of different compartments in space and time.