Principles of synthetic biology

In synthetic biology, biological cells and processes are dismantled and reassembled to make novel systems that do useful things. Designs are encoded by deoxyribonucleic acid (DNA); DNA makes biological (bio-)parts; bioparts are combined to make devices; devices are built into biological systems. Computers are used at all stages of the Design-Build-Test-Learn cycle, from mathematical modelling through to the use of robots for the automation of assembly and experimentation. Synthetic biology applies engineering principles of standardisation, modularity, and abstraction, enabling fast prototyping and the ready exchange of designs between synthetic biologists working around the world. Like toy building blocks, compatible modular designs enable bioparts to be combined and optimised easily; biopart specifications are shared in open registries. Synthetic biology is made possible due to major advances in DNA sequencing and synthesis technologies, and through knowledge gleaned in the field of systems biology. Systems biology aims to understand biology across scales, from the molecular and cellular, up to tissues and organisms, and describes cells as complex information-processing systems. By contrast, synthetic biology seeks to design and build its own systems. Applications of synthetic biology are wide-ranging but include impacting healthcare to improve diagnosis and make better treatments for disease; it seeks to improve the environment by finding novel ways to clean up pollution, make industrial processes for chemical synthesis sustainable, and remove the need for damaging farming practices by making better fertilisers. Synthetic biology has the potential to change the way we live and help us to protect the future of our planet.

Humidity mediated performance and material properties of orb weaving spider adhesive droplets

Capture thread glue droplets retain insects that strike an orb web and are key to the success of over 4,600 described spider species. Each droplet is a self-assembling adhesive system whose emergent biomechanical properties are centered on its viscoelastic, protein core. This bioadhesive is dependent on its surrounding hygroscopic aqueous layer for hydration and chemical conditioning. Consequently, a droplet's water content and adhesive performance track environmental humidity. We tested the hypothesis that natural selection has tuned a droplet's adhesive performance and material properties to a species' foraging humidity. At 55% relative humidity (RH) the adhesive properties of 12 species ranged from that of PEG-based hydrogels to that of silicone rubber, exhibiting a 1088-fold inter-specific difference in stiffness (0.02-21.76 MPa) and a 147-fold difference in toughness (0.14-20.51 MJ/m³). When tested over a 70% RH range, droplet extension lengths per protein core volume peaked at lower humidities in species from exposed, low humidity habitats, and at higher humidities in nocturnal species and those found in humid habitats. However, at the RH's where these species' maximum extension per protein volume indices were observed, the stiffness of most species' adhesive did not differ, documenting that selection has tuned elastic modulus by adjusting droplet hygroscopicity. This inverse relationship between droplet hygroscopicity and a species' foraging humidity ensures optimal adhesive stiffness. By characterizing the humidity responsiveness and properties of orb spider glue droplets, our study also profiles the range of its biomimetic potential. STATEMENT OF SIGNIFICANCE: Over 4,600 described species of orb weaving spider rely on tiny glue droplets in their webs to retain insect that the web intercepts. The aqueous layer that covers each droplet's core allows this adhesive to remain pliable and to stretch as an insect struggles to escape. The aqueous solution also attracts water from the air, causing the glue droplet's performance to change with humidity. By characterizing the droplet extensions and adhesive material properties of twelve species at relative humidities between of 20 and 90%, this study examined how this unique adhesive system responds to its environment and how it is tuned to the humidity of a species' habitat.

Advances in Plant-Derived Scaffold Proteins

Scaffold proteins form critical biomatrices that support cell adhesion and proliferation for regenerative medicine and drug screening. The increasing demand for such applications urges solutions for cost effective and sustainable supplies of hypoallergenic and biocompatible scaffold proteins. Here, we summarize recent efforts in obtaining plant-derived biosynthetic spider silk analogue and the extracellular matrix protein, collagen. Both proteins are composed of a large number of tandem block repeats, which makes production in bacterial hosts challenging. Furthermore, post-translational modification of collagen is essential for its function which requires co-transformation of multiple copies of human prolyl 4-hydroxylase. We discuss our perspectives on how the GAANTRY system could potentially assist the production of native-sized spider dragline silk proteins and prolyl hydroxylated collagen. The potential of recombinant scaffold proteins in drug delivery and drug discovery is also addressed.

Properties of orb weaving spider glycoprotein glue change during Argiope trifasciata web construction

An orb web’s prey capture thread relies on its glue droplets to retain insects until a spider can subdue them. Each droplet’s viscoelastic glycoprotein adhesive core extends to dissipate the forces of prey struggle as it transfers force to stiffer, support line flagelliform fibers. In large orb webs, switchback capture thread turns are placed at the bottom of the web before a continuous capture spiral progresses from the web’s periphery to its interior. To determine if the properties of capture thread droplets change during web spinning, we characterized droplet and glycoprotein volumes and material properties from the bottom, top, middle, and inner regions of webs. Both droplet and glycoprotein volume decreased during web construction, but there was a progressive increase in the glycoprotein’s Young’s modulus and toughness. Increases in the percentage of droplet aqueous material indicated that these increases in material properties are not due to reduced glycoprotein viscosity resulting from lower droplet hygroscopicity. Instead, they may result from changes in aqueous layer compounds that condition the glycoprotein. A 6-fold difference in glycoprotein toughness and a 70-fold difference in Young’s modulus across a web documents the phenotypic plasticity of this natural adhesive and its potential to inspire new materials.

Analysis of repetitive amino acid motifs reveals the essential features of spider dragline silk proteins

The extraordinary mechanical properties of spider dragline silk are dependent on the highly repetitive sequences of the component proteins, major ampullate spidroin 1 and 2 (MaSp2 and MaSp2). MaSp sequences are dominated by repetitive modules composed of short amino acid motifs; however, the patterns of motif conservation through evolution and their relevance to silk characteristics are not well understood. We performed a systematic analysis of MaSp sequences encompassing infraorder Araneomorphae based on the conservation of explicitly defined motifs, with the aim of elucidating the essential elements of MaSp1 and MaSp2. The results show that the GGY motif is nearly ubiquitous in the two types of MaSp, while MaSp2 is invariably associated with GP and di-glutamine (QQ) motifs. Further analysis revealed an extended MaSp2 consensus sequence in family Araneidae, with implications for the classification of the archetypal spidroins ADF3 and ADF4. Additionally, the analysis of RNA-seq data showed the expression of a set of distinct MaSp-like variants in genus Tetragnatha. Finally, an apparent association was uncovered between web architecture and the abundance of GP, QQ, and GGY motifs in MaSp2, which suggests a co-expansion of these motifs in response to the evolution of spiders' prey capture strategy.