Materials Synthetic Biology

Living natural materials have remarkable sensing abilities that translate external cues into functional changes of the material. The reconstruction of such sensing materials in bottom-up synthetic biology provides the opportunity to develop synthetic materials with life-like sensing and adaptation ability. Key to such functions are material modules that translate specific input signals into a biomolecular response. Here, we engineer a synthetic organelle based on liquid–liquid phase separation that translates a metabolic signal into the regulation of gene transcription. To this aim, we engineer the pyruvate-dependent repressor PdhR to undergo liquid–liquid phase separation in vitro by fusion to intrinsically disordered regions. We demonstrate that the resulting coacervates bind DNA harboring PdhR-responsive operator sites in a pyruvate dose-dependent and reversible manner. We observed that the activity of transcription units on the DNA was strongly attenuated following recruitment to the coacervates. However, the addition of pyruvate resulted in a reversible and dose-dependent reconstitution of transcriptional activity. The coacervate-based synthetic organelles linking metabolic cues to transcriptional signals represent a materials approach to confer stimulus responsiveness to minimal bottom-up synthetic biological systems and open opportunities in materials for sensor applications.

Materials that can be switched between a polycationic/antimicrobial and a polyzwitterionic/protein-repellent state have important applications, e.g., as biofilm-reducing coatings in medical devices. However, the lack of stability under storage and application conditions so far restricts the lifetime and efficiency of such materials. In this work, a polynorbornene-based polycarboxybetaine with an optimized molecular structure for improved hydrolytic stability is presented. The polymer is fully characterized on the molecular level. Surface-attached polymer networks are obtained by spin-coating and UV cross-linking. These coatings are highly uniform and demonstrate charge-switching in zeta-potential studies. Storage stability in the dry state, as well as in aqueous systems at pH 4.5 and 7.4 for 28 days, is demonstrated. At pH 8, hydrolytic degradation is observed. Overall, the materials are substantially more stable than the corresponding ester-based systems.

Neutrophils are innate immune cells that perpetually patrol the circulation and tissues. They sense and migrate toward invading microbes to initiate and orchestrate a robust immune response. Their highly reactive nature, driven by multiple and redundant receptor families recognizing bacterial components, makes them particularly sensitive to contaminants or nonsterile implants. This often leads to a neutrophil-driven foreign body reaction that shields the implant and triggers inflammation, collateral tissue damage, or even sepsis. This presents a significant challenge for living therapeutic materials, an innovative biomedical approach using genetically engineered bacteria encapsulated in natural or synthetic polymers. Since bacterial turnover inevitably releases pathogen-associated molecular patterns that activate neutrophils to mitigate or prevent a potent neutrophil response, living therapeutic material design strategies are required to protect the living therapeutic material from damage while maintaining its functionality. This review focuses on current strategies involving bacterial genetic engineering, immune-shielding materials and factors, and modified hydrogel-based systems to minimize immune recognition. Engineering the bacterial chassis to produce immune tolerance–inducing metabolites from commensals, modified pathogen-associated molecular patterns, and pathogen-associated molecular pattern–cleaving autolysins may enhance biocompatibility. A crucial aspect for clinical translation is robust biocontainment to prevent bacterial escape, ensuring living therapeutic material remains a safe and effective therapeutic platform. While the potential of the living therapeutic material concept lies in the development of tailored medicine specifically designed for a specific disease and enabling local, cost-effective, site- and stimulus-responsive treatment, balancing the neutrophil immune response remains an important milestone on the path to living therapeutic material for future biomedical applications.

Formyl peptide receptors (FPRs) are pattern recognition receptors well-known for bacterial pathogen sensing. We here identified activator and inhibitor motifs for FPRs that are present on surface proteins of various viral pathogens. Peptides containing these motifs interact with all FPR family members and modulate various important immune functions in innate immune cells. Viral breakdown products comprising these motifs were found in patients with COVID-19. In the spike protein, many activators are found in highly mutagenic regions, whereas the inhibitor motif is located in a conserved domain that also exists in further unrelated viruses. The physiochemical properties of FPR1 activators correlate with the occurrence of protein aggregation hotspots. Such hotspots are present on various surface proteins of unrelated viruses that can also activate FPRs. This points toward a general contribution of FPRs in modulating antiviral immune responses during many distinct viral infections.

Long-lasting polypore fungi are significant producers of terpene cyclases of high interest for medicinal or biotechnological applications. Following the 1000 Fungal Genomes initiative launched by the Joint Genome Institute, the genome of Cubamyces (C.) menziesii and identified 18 genes encoding sesquiterpene cyclases (STCs) is explored. In a search for robust catalysts suitable for practical applications, the 18 codon-optimized open reading frames are cloned and overproduced the C. menziesii STCs in Escherichia coli. In ten cases, the catalytically active enzyme is purified and tested with three chemically synthesized linear diphosphates: geranyl diphosphate, farnesyl diphosphate (FDP), and geranylgeranyl diphosphate. Only FDP proved to be a substrate for these 10 enzymes. The product specificity of all these enzymes is determined by (GC-MS) gas chromatography mass spectrometry and (NMR) nuclear magnetic resonance analysis. Among the 10 enzymes, four produced a predominant compound, four yielded two main compounds, and the remaining two acted as a multiproduct catalysts. This work sheds light on the potential sesquiterpenes involved in the chemical ecology of the polypore C. menziesii and provides evidence for the potential of Polyporales fungi in the identification of new sesquiterpene cyclase activities.

Elastocaloric technology is a new way to heat and cool spaces by using stretchy metals, called shape-memory alloys, instead of harmful refrigerant gases. When these metals are squeezed or stretched, they heat up; and when they relax, they cool down. This process is called the elastocaloric effect and it is more energy efficient than traditional cooling systems, making it a cleaner, greener alternative. Elastocaloric systems could cool homes, schools, and workplaces, and they could refrigerate food and medicine in areas with limited electricity. Researchers are also testing this technology for cooling and heating of electric vehicles, where it could help conserve battery life, and for heating buildings in colder climates. Despite its promise, elastocaloric technology faces challenges, such as improving the durability of materials and making the shape-memory alloys more affordable. With continued research, this technology could someday help to reduce greenhouse gas emissions, lower energy costs, and bring life-saving cooling to more people all over the world.

Methods for the precise temporal control of cell surface receptor activation are indispensable for the investigation of signaling processes in mammalian cells. Optogenetics enables such precise control, but its application in primary cells is limited by the imperative for genetic manipulation of target cells. We here describe a method that overcomes this obstacle and enables the precise activation of the T cell receptor in nongenetically engineered human T cells by light. Our optogenetic receptor activation system OptoREACT employs a TCR-specific scFv fused to PIF6 that interacts with tetramerized PhyB in a light-dependent manner and thereby clusters and activates the T cell receptor in response to red light. OptoREACT not only omits genetic manipulation of the target cell but, because of its modular nature, is likely applicable to a broad range of oligomerization-activated cell surface receptors.

The construction and assembly of information-processing biomaterials are limited by the need for laborious assembly of various circuits. A new framework to assemble protein-based elements encoding complex Boolean operations enables user-defined release of biomolecules from these materials.

Molecular optogenetics allows the control of molecular signaling pathways in response to light. This enables the analysis of the kinetics of signal activation and propagation in a spatially and temporally resolved manner. A key strategy for such control is the light-inducible clustering of signaling molecules, which leads to their activation and subsequent downstream signaling. In this work, an optogenetic approach is developed for inducing graded clustering of different proteins that are fused to eGFP, a widely used protein tag. To this aim, an eGFP-specific nanobody is fused to Cryptochrome 2 variants engineered for different orders of cluster formation. This is exemplified by clustering eGFP-IKKα and eGFP-IKKβ, thereby achieving potent and reversible activation of NF-κB signaling. It is demonstrated that this approach can activate downstream signaling via the endogenous NF-κB pathway and is thereby capable of activating both an NF-κB-responsive reporter construct as well as endogenous NF-κB-responsive target genes as analyzed by RNA sequencing. The generic design of this system is likely transferable to other signaling pathways to analyze the kinetics of signal activation and propagation.

Formaldehyde is the smallest existing aldehyde, a highly reactive color less gas at room temperature and ubiquitously present in our atmosphere. Because of its reactivity leading to the crosslinking of macromolecules like proteins, it is widely used in industrial applications, but also in cell biology in order to preserve cells and tissues for further analysis. In this work, we show that formaldehyde releasing solutions commonly used for fixation of cells, can diffuse via the gas phase to the neighboring well and influence signaling processes in the therein cultured cells. To analyze this effect, we utilized a stable reporter cell line for YAP signaling or a gene expression-based reporter for activation of the NF-κB pathway. We could show that next to formaldehyde, also glutaraldehyde and acetaldehyde were able to activate those signaling pathways. Additionally, especially the stable reporter cell line based on YAP signaling can also be used as sensor for bioavailable formaldehyde, being highly sensitive, easy to use, and reversible. The observed impact of formaldehyde on cellular signaling underscores the need for careful planning of experimental protocols and emphasizes the importance of implementing proper controls when utilizing this reagent in cellular signaling analyses.