Nature-Inspired Circular-Economy Recycling for Proteins: Proof of Concept

Nature-inspired recycling of a protein mixture into a green fluorescent protein-based hydrogel

Protein-based materials are biocompatible and have a variety of remarkable properties; consequently, they are finding more and more applications. Nature recycles proteins in multiple ways, ranging from bio-degradation (a slow approach) to fast recycling of protein metabolism. The latter is a wonderful example because a random mixture of proteins gets digested into amino acids (AAs), the fundamental building blocks of proteins. These AAs are then used by cells to produce whichever protein is needed at the time of synthesis. Seen through the lens of recycling, this process transforms a random mixture into something not necessarily present at the start but needed at the moment of recycling. We have recently shown that the process of protein recycling can be performed in vitro and called it NaCRe (Nature Inspired Circular Recycling). In a previous NaCRe proof-of-concept experiment, we started with various protein mixtures but were able to produce only small quantities of recycled protein, in the microgram scale. Here, we show that NaCRe can be used to convert milligrams of a protein mixture containing one of the most common protein materials (silk) into a milligram of an hydrogel made of green fluorescent protein (GFP). We show that in order for NaCRe to be efficient the starting protein mixture must contain a good balance of all AAs and discuss the challenges encountered when scaling up NaCRe.

Integrated translation and metabolism in a partially self-synthesizing biochemical network

One of the hallmarks of living organisms is their capacity for self-organization and regeneration, which requires a tight integration of metabolic and genetic networks. We sought to construct a linked metabolic and genetic network in vitro that shows such lifelike behavior outside of a cellular context and generates its own building blocks from nonliving matter. We integrated the metabolism of the crotonyl-CoA/ethyl-malonyl-CoA/hydroxybutyryl-CoA cycle with cell-free protein synthesis using recombinant elements. Our network produces the amino acid glycine from CO2 and incorporates it into target proteins following DNA-encoded instructions. By orchestrating ~50 enzymes we established a basic cell-free operating system in which genetically encoded inputs into a metabolic network are programmed to activate feedback loops allowing for self-integration and (partial) self-regeneration of the complete system.

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.

Recycling of Polymerase Chain Reaction (PCR) Kits

Polymerase chain reaction (PCR) kits have been used as common diagnosing tools during the outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, with daily worldwide usage in the millions. It is well known that at the beginning of the pandemic, there was a shortage of PCR kits. So far, the ecosystem of a PCR kit is linear use; that is, kits are produced, used once, and disposed of as biolab waste. Here, we show that to mitigate the risk of future shortages, it is possible to envision recyclable PCR kits based on a more sustainable use of nucleic acid resources. A PCR kit is mainly composed of primers, nucleotides, and enzymes. In the case of a positive test, the free nucleotides are polymerized onto the primers to form longer DNA strands. Our approach depolymerizes such strands, keeping the primers and regenerating the nucleotides, i.e., returning the nucleic acid materials to the original state. The polymerized long DNA strands are hydrolyzed into nucleotide monophosphates that are then phosphorylated into triphosphates using a method that is developed from a recent publication. We used oligonucleotides with a 3'-terminal phosphorothioate (PS) backbone modification as nonhydrolyzable PCR primers, which are able to undergo the recycling process unchanged. The nuclease resistance of oligonucleotides with a ribose sugar modification was also evaluated, which showed worse recycling efficiency than PS-modified oligonucleotides. We successfully recycled both PCR primers and nucleotide monomers (∼75% yield). We demonstrate that the method allows for the direct reuse of PCR kits. We also show that the recycled primers can be isolated and then added to endpoint or quantitative PCR. This recycling approach provides a new path for circularly reusing nucleic acid materials in PCR kits.

The Long Road to a Synthetic Self-Replicating Central Dogma

The construction of a biochemical system capable of self-replication is a key objective in bottom-up synthetic biology. Throughout the past two decades, a rapid progression in the design of in vitro cell-free systems has provided valuable insight into the requirements for the development of a minimal system capable of self-replication. The main limitations of current systems can be attributed to their macromolecular composition and how the individual macromolecules use the small molecules necessary to drive RNA and protein synthesis. In this Perspective, we discuss the recent steps that have been taken to generate a minimal cell-free system capable of regenerating its own macromolecular components and maintaining the homeostatic balance between macromolecular biogenesis and consumption of primary building blocks. By following the flow of biological information through the central dogma, we compare the current versions of these systems to date and propose potential alterations aimed at designing a model system for self-replicative synthetic cells.

Optimization of Technological Parameters of the Process of Forming Therapeutic Biopolymer Nanofilled Films

The prospects of using biopolymer nano-containing films for wound healing were substantiated. The main components of biopolymer composites are gelatin, polyvinyl alcohol, glycerin, lactic acid, distilled water, and zinc oxide (ZnO) nanoparticles (NPs). Biopolymer composites were produced according to various technological parameters using a mould with a chrome coating. The therapeutic properties of biopolymer films were evaluated by measuring the diameter of the protective effect. Physico-mechanical properties were studied: elasticity, vapour permeability, degradation time, and swelling. To study the influence of technological parameters of the formation process of therapeutic biopolymer nanofilled films on their therapeutic and physico-mechanical properties, the planning of the experiment was used. According to the results of the experiments, mathematical models of the second-order were built. The optimal values of technological parameters of the process are determined, which provide biopolymer nanofilled films with maximum healing ability (diameter of protective action) and sufficiently high physical and mechanical properties: elasticity, vapour permeability, degradation time and swelling. The research results showed that the healing properties of biopolymer films mainly depend on the content of ZnO NPs. Degradation of these biopolymer films provides dosed drug delivery to the affected area. The products of destruction are carbon dioxide, water, and a small amount of ZnO in the bound state, which indicates the environmental safety of the developed biopolymer film.

Methacrylated Bovine Serum Albumin and Tannic Acid Composite Materials for Three-Dimensional Printing Tough and Mechanically Functional Parts

Nature uses proteins as building blocks to create three-dimensional (3D) structural components (like spiderwebs and tissue) that are recycled within a closed loop. Furthermore, it is difficult to replicate the mechanical properties of these 3D architectures within synthetic systems. In the absence of biological machinery, protein-based materials can be difficult to process and can have a limited range of mechanical properties. Herein, we present an additive manufacturing workflow to fabricate tough, protein-based composite hydrogels and bioplastics with a range of mechanical properties. Briefly, methacrylated bovine-serum-albumin-based aqueous resins were 3D-printed using a commercial vat photopolymerization system. The printed structures were then treated with tannic acid to introduce additional non-covalent interactions and form tough hydrogels. The hydrogel material could be sutured and withstand mechanical load, even after immersion in water for 24 h. Additionally, a denaturing thermal cure could be used to virtually eliminate rehydration of the material and form a bioplastic. To highlight the functionality of this material, a bioplastic screw was 3D-printed and driven into wood without damage to the screw. Moreover, the 3D-printed constructs enzymatically degraded up to 85% after 30 days in pepsin solution. Thus, these protein-based 3D-printed constructs show great potential for biomedical devices that degrade in situ.

Recycling of Load-Bearing 3D Printable Double Network Granular Hydrogels

Sustainable materials, such as recyclable polymers, become increasingly important as they are often environmentally friendlier than their one-time-use counterparts. In parallel, the trend toward more customized products demands for fast prototyping methods which allow processing materials into 3D objects that are often only used for a limited amount of time yet, that must be mechanically sufficiently robust to bear significant loads. Soft materials that satisfy the two rather contradictory needs remain to be shown. Here, the authors introduce a material that simultaneously fulfills both requirements, a 3D printable, recyclable double network granular hydrogel (rDNGH). This hydrogel is composed of poly(2-acrylamido-2-methylpropane sulfonic acid) microparticles that are covalently crosslinked through a disulfide-based percolating network. The possibility to independently degrade the percolating network, with no harm to the primary network contained within the microgels, renders the recovery of the microgels efficient. As a result, the recycled material pertains a stiffness and toughness that are similar to those of the pristine material. Importantly, this process can be extended to the fabrication of recyclable hard plastics made of, for example, dried rDNGHs. The authors envision this approach to serve as foundation for a paradigm shift in the design of new sustainable soft materials and plastics.