Cytoskeletal and Actin-Based Polymerization Motors and Their Role in Minimal Cell Design

Exerting pulling forces in fluids by directional disassembly of microcrystalline fibres

Biomolecular polymerization motors are biochemical systems that use supramolecular (de-)polymerization to convert chemical potential into useful mechanical work. With the intent to explore new chemomechanical transduction strategies, here we show a synthetic molecular system that can generate forces via the controlled disassembly of self-organized molecules in a crystal lattice, as they are freely suspended in a fluid. An amphiphilic monomer self-assembles into rigid, high-aspect-ratio microcrystalline fibres. The assembly process is regulated by a coumarin-based pH switching motif. The microfibre crystal morphology determines the monomer reactivity at the interface, resulting in anisotropic etching. This effect exerts a directional pulling force on microscopic beads adsorbed on the crystal surface through weak multivalent interactions. We use optical-tweezers-based force spectroscopy to extract mechanistic insights into this process, quantifying a stall force of 2.3 pN (±0.1 pN) exerted by the ratcheting mechanism produced by the disassembly of the microfibres.

Dynamic self-assembly of compartmentalized DNA nanotubes

Bottom-up synthetic biology aims to engineer artificial cells capable of responsive behaviors by using a minimal set of molecular components. An important challenge toward this goal is the development of programmable biomaterials that can provide active spatial organization in cell-sized compartments. Here, we demonstrate the dynamic self-assembly of nucleic acid (NA) nanotubes inside water-in-oil droplets. We develop methods to encapsulate and assemble different types of DNA nanotubes from programmable DNA monomers, and demonstrate temporal control of assembly via designed pathways of RNA production and degradation. We examine the dynamic response of encapsulated nanotube assembly and disassembly with the support of statistical analysis of droplet images. Our study provides a toolkit of methods and components to build increasingly complex and functional NA materials to mimic life-like functions in synthetic cells.

The use of giant unilamellar vesicles to study functional properties of pore-forming toxins

Pore-forming toxins (PFTs) act upon lipid membranes and appropriate model systems are of great importance in researching these proteins. Giant unilamellar vesicles (GUVs) are an excellent model membrane system to study interactions between lipids and proteins. Their main advantage is the size comparable to cells, which means that GUVs can be observed directly under the light microscope. Many PFTs properties can be studied by using GUVs, such as binding specificity, membrane reorganization upon protein binding and oligomerization, pore properties and mechanism of pore formation. GUVs also represent a good model for biotechnological approaches, e.g., in applications in synthetic biology and medicine. Each research area has its own demands for GUVs properties, so several different approaches for GUVs preparations have been developed and will be discussed in this chapter.

Tropomodulin1 Expression Increases Upon Maturation in Dendritic Cells and Promotes Their Maturation and Immune Functions

Dendritic cells (DCs) are the most potent antigen-presenting cells. Upon maturation, DCs express costimulatory molecules and migrate to the lymph nodes to present antigens to T cells. The actin cytoskeleton plays key roles in multiple aspects of DC functions. However, little is known about the mechanisms and identities of actin-binding proteins that control DC maturation and maturation-associated functional changes. Tropomodulin1 (Tmod1), an actin-capping protein, controls actin depolymerization and nucleation. We found that Tmod1 was expressed in bone marrow-derived immature DCs and was significantly upregulated upon lipopolysaccharide (LPS)-induced DC maturation. By characterizing LPS-induced mature DCs (mDCs) from Tmod1 knockout mice, we found that compared with Tmod1+/+ mDCs, Tmod1-deficient mDCs exhibited lower surface expression of costimulatory molecules and chemokine receptors and reduced secretion of inflammatory cytokines, suggesting that Tmod1 deficiency retarded DC maturation. Tmod1-deficient mDCs also showed impaired random and chemotactic migration, deteriorated T-cell stimulatory ability, and reduced F-actin content and cell stiffness. Furthermore, Tmod1-deficient mDCs secreted high levels of IFN-β and IL-10 and induced immune tolerance in an experimental autoimmune encephalomyelitis (EAE) mouse model. Mechanistically, Tmod1 deficiency affected TLR4 signaling transduction, resulting in the decreased activity of MyD88-dependent NFκB and MAPK pathways but the increased activity of the TRIF/IRF3 pathway. Rescue with exogenous Tmod1 reversed the effect of Tmod1 deficiency on TLR4 signaling. Therefore, Tmod1 is critical in regulating DC maturation and immune functions by regulating TLR4 signaling and the actin cytoskeleton. Tmod1 may be a potential target for modulating DC functions, a strategy that would be beneficial for immunotherapy for several diseases.

Intestinal Inflammation as a Dysbiosis of Energy Procurement: New Insights into an Old Topic

Inflammatory bowel disease (IBD) coincides with profound shifts in microbiota and host metabolic energy supply and demand. The gastrointestinal epithelium is anatomically positioned to provide a selective barrier between the anaerobic luminal microbiota and host lamina propria, with the microbiota and epithelium participating in an intricate energy exchange necessary for homeostasis. Maintenance and restoration of the barrier requires high energy flux and places significant demands on available substrates to generate ATP. It is recently appreciated that components of the microbiota contribute significantly to a multitude of biochemical pathways within and outside of the mucosa. Decades-old studies have appreciated that byproducts of the microbiota provide essential sources of energy to the intestinal epithelium, especially the colon. More recent work has unveiled the existence of numerous microbial-derived metabolites that support energy procurement within the mucosa. It is now appreciated that disease-associated shifts in the microbiota, termed dysbiosis, places significant demands on energy acquisition within the mucosa. Here, we review the topic of host- and microbial-derived components that influence tissue energetics in health and during disease.

Encapsulation of the cytoskeleton: towards mimicking the mechanics of a cell

The cytoskeleton of a cell controls all the aspects of cell shape changes and motility from its physiological functions for survival to reproduction to death. The structure and dynamics of the cytoskeletal components: actin, microtubules, intermediate filaments, and septins - recently regarded as the fourth member of the cytoskeleton family - are conserved during evolution. Such conserved and effective control over the mechanics of the cell makes the cytoskeletal components great candidates for in vitro reconstitution and bottom-up synthetic biology studies. Here, we review the recent efforts in reconstitution of the cytoskeleton in and on membrane-enclosed biomimetic systems and argue that co-reconstitution and synergistic interplay between cytoskeletal filaments might be indispensable for efficient mechanical functionality of active minimal cells. Further, mechanical equilibrium in adherent eukaryotic cells is achieved by the formation of integrin-based focal contacts with extracellular matrix (ECM) and the transmission of stresses generated by actomyosin contraction to ECM. Therefore, a minimal mimic of such balance of forces and quasi-static kinetics of the cell by bottom-up reconstitution requires a careful construction of contractile machineries and their link with adhesive contacts. In this review, in addition to cytoskeletal crosstalk, we provide a perspective on reconstruction of cell mechanical equilibrium by reconstitution of cortical actomyosin networks in lipid membrane vesicles adhered on compliant substrates and also discuss future perspectives of this active research area.

Reconstitution and Coupling of DNA Replication and Segregation in a Biomimetic System

A biomimetic system capable of replication and segregation of genetic material constitutes an essential component for the future design of a minimal synthetic cell. Here we have used the simple T7 bacteriophage system and the plasmid-derived ParMRC system to establish in vitro DNA replication and DNA segregation, respectively. These processes were incorporated into biomimetic compartments providing an enclosed reaction space. The functional lifetime of the encapsulated segregation system could be prolonged by equipping it with ATP-regenerating and oxygen-scavenging systems. Finally, we showed that DNA replication and segregation processes could be coupled in vitro by using condensed DNA nanoparticles resulting from DNA replication. ParM spindles extended over tens of micrometers and could thus be used for segregation in compartments that are significantly longer than bacterial cell size. Overall, this work demonstrates the successful bottom-up assembly and coupling of molecular machines that mediate replication and segregation, thus providing an important step towards the development of a fully functional minimal cell.