Genetic Code Expansion of the Silkworm Bombyx mori to Functionalize Silk Fiber

Silk Bioconjugates: From Chemistry and Concept to Application

Medical silks have captured global interest. While silk sutures have a long track record in humans, silk bioconjugates are still in preclinical development. This perspective examines key advances in silk bioconjugation, including the fabrication of silk-protein conjugates, bioconjugated silk particles, and bioconjugated substrates to enhance cell-material interactions in two and three dimensions. Many of these systems rely on chemical modification of the silk biopolymer, often using carbodiimide and reactive ester chemistries. However, recent progress in enzyme-mediated and click chemistries has expanded the molecular toolbox to enable biorthogonal, site-specific conjugation in a single step when combined with recombinant silk fibroin tagged with noncanonical amino acids. This perspective outlines key strategies available for chemical modification, compares the resulting silk conjugates to clinical benchmarks, and outlines open questions and areas that require more work. Overall, this assessment highlights a domain of new sunrise capabilities and development opportunities for silk bioconjugates that may ultimately offer new ways of delivering improved healthcare.

Transgenic modifications of silkworms as a means to obtain therapeutic biomolecules and protein fibers with exceptional properties

Transgenic modification of Bombyx mori silkworms is a benign approach for the production of silk fibers with extraordinary properties and also to generate therapeutic proteins and other biomolecules for various applications. Silk fibers with fluorescence lasting more than a year, natural protein fibers with strength and toughness exceeding that of spider silk, proteins and therapeutic biomolecules with exceptional properties have been developed using transgenic technology. The transgenic modifications have been done primarily by modifying the silk sericin and fibroin genes and also the silk producing glands. Although the genetic modifications were typically performed using the sericin 1 and other genes, newer techniques such as CRISPR/Cas9 have enabled successful modifications of both the fibroin H-chain and L-chain. Such modifications have led to the production of therapeutic proteins and other biomolecules in reasonable quantities at affordable costs for tissue engineering and other medical applications. Transgenically modified silkworms also have distinct and long-lasting fluorescence useful for bioimaging applications. This review presents an overview of the transgenic techniques for modifications of B. mori silkworms and the properties obtained due to such modifications with particular focus on production of growth factors, fluorescent proteins, and high performance protein fibers.

Unique Material Properties of Bombyx mori Silk Fiber Incorporated with 3-Azidotyrosine

Silk fiber produced by the silkworm Bombyx mori is a nature-derived proteinous fiber with excellent mechanical strength and broad biocompatibility. To alter its material properties and make it more suitable for textile, biomedical, and electronics applications, chemical modifications and genetic engineering methods have been extensively studied. Here, we report that the translational incorporation of a synthetic amino acid, 3-azidotyrosine (3-AzTyr), into B. mori silk fiber can improve its material properties. Such an incorporation considerably increased the fiber's mechanical strength and remarkably changed its solubility, whereas its crystalline hierarchical structure was not perturbed, as shown by X-ray analyses. These changes were probably caused by the intra- and/or intermolecular crosslinkings involving the azido group of 3-AzTyr during the degumming process to remove a coating protein. These findings indicate that the incorporation of synthetic amino acids could be an efficient method to improve the properties of silk-based materials.

Synthetic biology-guided design and biosynthesis of protein polymers for delivery

Vehicles derived from genetically engineered protein polymers have gained momentum in the field of biomedical engineering due to their unique designability, remarkable biocompatibility and excellent biodegradability. However, the design and production of these protein polymers with on-demand sequences and supramolecular architectures remain underexplored, particularly from a synthetic biology perspective. In this review, we summarize the state-of-the art strategies for constructing the highly repetitive genes encoding the protein polymers, and highlight the advanced approaches for metabolically engineering expression hosts towards high-level biosynthesis of the target protein polymers. Finally, we showcase the typical protein polymers utilized to fabricate delivery vehicles.

Building biomaterials through genetic code expansion

Genetic code expansion (GCE) enables directed incorporation of noncoded amino acids (NCAAs) and unnatural amino acids (UNAAs) into the active core that confers dedicated structure and function to engineered proteins. Many protein biomaterials are tandem repeats that intrinsically include NCAAs generated through post-translational modifications (PTMs) to execute assigned functions. Conventional genetic engineering approaches using prokaryotic systems have limited ability to biosynthesize functionally active biomaterials with NCAAs/UNAAs. Codon suppression and reassignment introduce NCAAs/UNAAs globally, allowing engineered proteins to be redesigned to mimic natural matrix-cell interactions for tissue engineering. Expanding the genetic code enables the engineering of biomaterials with catechols - growth factor mimetics that modulate cell-matrix interactions - thereby facilitating tissue-specific expression of genes and proteins. This method of protein engineering shows promise in achieving tissue-informed, tissue-compliant tunable biomaterials.

Expanding the chemical repertoire of protein-based polymers for drug-delivery applications

Expanding the chemical repertoire of natural and artificial protein-based polymers (PBPs) can enable the production of sequence-defined, yet chemically diverse, biopolymers with customized or new properties that cannot be accessed in PBPs composed of only natural amino acids. Various approaches can enable the expansion of the chemical repertoire of PBPs, including chemical and enzymatic treatments or the incorporation of unnatural amino acids. These techniques are employed to install a wide variety of chemical groups-such as bio-orthogonally reactive, cross-linkable, post-translation modifications, and environmentally responsive groups-which, in turn, can facilitate the design of customized PBP-based drug-delivery systems with modified, fine-tuned, or entirely new properties and functions. Here, we detail the existing and emerging technologies for expanding the chemical repertoire of PBPs and review several chemical groups that either demonstrate or are anticipated to show potential in the design of PBP-based drug delivery systems. Finally, we provide our perspective on the remaining challenges and future directions in this field.

Genome recoding strategies to improve cellular properties: mechanisms and advances

The genetic code, once believed to be universal and immutable, is now known to contain many variations and is not quite universal. The basis for genome recoding strategy is genetic code variation that can be harnessed to improve cellular properties. Thus, genome recoding is a promising strategy for the enhancement of genome flexibility, allowing for novel functions that are not commonly documented in the organism in its natural environment. Here, the basic concept of genetic code and associated mechanisms for the generation of genetic codon variants, including biased codon usage, codon reassignment, and ambiguous decoding, are extensively discussed. Knowledge of the concept of natural genetic code expansion is also detailed. The generation of recoded organisms and associated mechanisms with basic targeting components, including aminoacyl-tRNA synthetase-tRNA pairs, elongation factor EF-Tu and ribosomes, are highlighted for a comprehensive understanding of this concept. The research associated with the generation of diverse recoded organisms is also discussed. The success of genome recoding in diverse multicellular organisms offers a platform for expanding protein chemistry at the biochemical level with non-canonical amino acids, genetically isolating the synthetic organisms from the natural ones, and fighting viruses, including SARS-CoV2, through the creation of attenuated viruses. In conclusion, genome recoding can offer diverse applications for improving cellular properties in the genome-recoded organisms.

Application of Bombyx mori Silk Fibroin Films for Liquid-Crystal Devices

Biocompatible and biodegradable silk fibroin films show promise as an eco-friendly biomaterial with excellent mechanical, thermal, and optical transparency properties. In contrast, polyimide (PI) films adopted in the liquid-crystal display (LCD) industry for aligning LC molecules are synthesized using toxic chemicals, which are nonrecyclable and nonbiodegradable. In this work, Bombyx mori silk fibroin films are fabricated from the aqueous solution and applied as alignment films for LCDs. The thermal properties of the prepared regenerated silk fibroin materials under different heat treatment temperatures are investigated using differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). The crystallinity of different heat-treated silk fibroin materials is determined by infrared spectroscopy. The silk fibroin film treated at a higher temperature exhibits better thermal stability due to the higher crystallinity of the β-form structure. The LCDs using silk fibroin alignment films show a low pretilt angle of 0.5° and an anchoring energy of ∼10^-3 J/m² similar to those of the conventional polyimide films.

Click Decoration of Bombyx mori Silk Fibroin for Cell Adhesion Control

Silk fibroin produced by the domesticated silkworm, Bombyx mori, has been studied widely as a substrate for tissue engineering applications because of its mechanical robustness and biocompatibility. However, it is often difficult to precisely tune silk fibroin's biological properties due to the lack of easy, reliable, and versatile methodologies for decorating it with functional molecules such as those of drugs, polymers, peptides, and enzymes necessary for specific applications. In this study we applied an azido-functionalized silk fibroin, AzidoSilk, produced by a state-of-the-art biotechnology, genetic code expansion, to produce silk fibroin decorated with cell-repellent polyethylene glycol (PEG) chains for controlling the cell adhesion property of silk fibroin film. Azido groups can act as selective handles for chemical reactions such as a strain-promoted azido-alkyne cycloaddition (SPAAC), known as a click chemistry reaction. We found that azido groups in AzidoSilk film were selectively decorated with PEG chains using SPAAC. The PEG-decorated film demonstrated decreased cell adhesion depending on the lengths of the PEG chains. Azido groups in AzidoSilk can be decomposed by UV irradiation. By partially decomposing azido groups in AzidoSilk film in a spatially controlled manner using photomasks, cells could be spatially arranged on the film. These results indicated that SPAAC could be an easy, reliable, and versatile methodology to produce silk fibroin substrates having adequate biological properties.

Transgenic and Diet-Enhanced Silk Production for Reinforced Biomaterials: A Metamaterial Perspective

Silk fibers, which are protein-based biopolymers produced by spiders and silkworms, are fascinating biomaterials that have been extensively studied for numerous biomedical applications. Silk fibers often have remarkable physical and biological properties that typical synthetic materials do not exhibit. These attributes have prompted a wide variety of silk research, including genetic engineering, biotechnological synthesis, and bioinspired fiber spinning, to produce silk proteins on a large scale and to further enhance their properties. In this review, we describe the basic properties of spider silk and silkworm silk and the important production methods for silk proteins. We discuss recent advances in reinforced silk using silkworm transgenesis and functional additive diets with a focus on biomedical applications. We also explain that reinforced silk has an analogy with metamaterials such that user-designed atypical responses can be engineered beyond what naturally occurring materials offer. These insights into reinforced silk can guide better engineering of superior synthetic biomaterials and lead to discoveries of unexplored biological and medical applications of silk.

Characterization and Scaled-Up Production of Azido-Functionalized Silk Fiber Produced by Transgenic Silkworms with an Expanded Genetic Code

The creation of functional materials from renewable resources has attracted much interest. We previously reported on the genetic code expansion of the domesticated silkworm Bombyx mori to functionalize silk fiber with synthetic amino acids such as 4-azido-L-phenylalanine (AzPhe). The azido groups act as selective handles for biorthogonal chemical reactions. Here we report the characterization and scaled-up production of azido-functionalized silk fiber for textile, healthcare, and medical applications. To increase the productivity of azido-functionalized silk fiber, the original transgenic line was hybridized with a high silk-producing strain. The F₁ hybrid produced circa 1.5 times more silk fibroin than the original transgenic line. The incorporation efficiency of AzPhe into silk fibroin was retained after hybridization. The tensile properties of the azido-functionalized silk fiber were equal to those of normal silk fiber. Scaled-up production of the azido-functionalized silk fiber was demonstrated by rearing circa 1000 transgenic silkworms. Differently-colored fluorescent silk fibers were successfully prepared by click chemistry reactions, demonstrating the utility of the azido-functionalized silk fiber for developing silk-based materials with desired functions.

Biological Engineered Living Materials: Growing Functional Materials with Genetically Programmable Properties

Natural biological materials exhibit remarkable properties: self-assembly from simple raw materials, precise control of morphology, diverse physical and chemical properties, self-repair, and the ability to sense-and-respond to environmental stimuli. Despite having found numerous uses in human industry and society, the utility of natural biological materials is limited. But, could it be possible to genetically program microbes to create entirely new and useful biological materials? At the intersection between microbiology, material science, and synthetic biology, the emerging field of biological engineered living materials (ELMs) aims to answer this question. Here we review recent efforts to program cells to produce living materials with novel functional properties, focusing on microbial systems that can be engineered to grow materials and on new genetic circuits for pattern formation that could be used to produce the more complex systems of the future.

Silkworm silk-based materials and devices generated using bio-nanotechnology

Silks are natural fibrous protein polymers that are spun by silkworms and spiders. Among silk variants, there has been increasing interest devoted to the silkworm silk of B. mori, due to its availability in large quantities along with its unique material properties. Silk fibroin can be extracted from the cocoons of the B. mori silkworm and combined synergistically with other biomaterials to form biopolymer composites. With the development of recombinant DNA technology, silks can also be rationally designed and synthesized via genetic control. Silk proteins can be processed in aqueous environments into various material formats including films, sponges, electrospun mats and hydrogels. The versatility and sustainability of silk-based materials provides an impressive toolbox for tailoring materials to meet specific applications via eco-friendly approaches. Historically, silkworm silk has been used by the textile industry for thousands of years due to its excellent physical properties, such as lightweight, high mechanical strength, flexibility, and luster. Recently, due to these properties, along with its biocompatibility, biodegradability and non-immunogenicity, silkworm silk has become a candidate for biomedical utility. Further, the FDA has approved silk medical devices for sutures and as a support structure during reconstructive surgery. With increasing needs for implantable and degradable devices, silkworm silk has attracted interest for electronics, photonics for implantable yet degradable medical devices, along with a broader range of utility in different device applications. This Tutorial review summarizes and highlights recent advances in the use of silk-based materials in bio-nanotechnology, with a focus on the fabrication and functionalization methods for in vitro and in vivo applications in the field of tissue engineering, degradable devices and controlled release systems.