Extreme diversity, conservation, and convergence of spider silk fibroin sequences

Elastomeric behavior of the Bombyx mori fibroin (GAGAGS)n tandem motifs

The mechanical properties of tandems composed by a repetition of the -GAGAGS- motif characteristic of Bombyx mori silk fibroin are explored using molecular dynamics simulations. For each tandem the calculation starts from the configuration reached upon minimizing the initial energy and proceeds by determining representative stationary states obtained from molecular dynamics simulations at a temperature of T = 300 K. Subsequently, the tandems are loaded by applying force to the α-carbon atoms at their ends and the force-displacement curve is built from the force exerted on the tandem as a function of the end-to-end distance between these atoms. The results obtained reveal two regimes as a function of the number of repetitions: tandems with one or two repetitions do not show a characteristic elastomeric behavior, while the curves calculated for tandems with a number of repetitions of three or greater can be fitted to the theoretical curves of a freely jointed chain.

Scale up of fermentation of recombinant Escherichia coli for efficient production of spider drag silk protein MaSp1s and its dimers

BACKGROUND

Spider dragline silk exhibits ultrahigh tensile strength and excellent ductility, making it one of the best-performing natural biomaterials. The major ampullate spidroin (MaSp1) has promising applications in the biomedical, chemical, and military industries owing to its good biocompatibility, biodegradability, and low immunogenicity. The generation of recombinant spidroin can significantly facilitate its scaled production but has several challenges, including the high cost of the downstream spidroin solubilization process and the resulting toxicity due to the use of organic solvents. Unlike common MaSp, MaSp short (MaSp1s) from Cyrtophoramoluccensis is a low-molecular-weight spidroin, lacking the typical repetitive sequences and long poly(A) motif. These features enable the heterologous production of soluble spidroin.

RESULTS

In this study, rMaSp1 and its dimer rMaSp1s-2Core were expressed in soluble form by introducing the SUMO fusion tag and the self-shearing peptide intein. To improve the yield of recombinant spidroin using shake-flask fermentation, response surface analysis was used to optimize the conditions. The yields of rMaSp1 and rMaSp1s-2Core were 218.9 and 95.76 mg/L, respectively. Subsequently, fermentation was scaled up in a 5 L fermenter after adding metal ions and other growth factors to the medium. The optimal inoculation amount, induction temperature, loaded liquid, and feeding strategy were explored. Finally, the yields of rMaSp1 and rMaSp1s-2Core reached 1,112.2 and 297.8 mg/L, respectively. Furthermore, the dimerization of rMaSp1 monomers was achieved by introducing disulfide bonds via exogenous cysteine residues in the C-terminal domain. The secondary structure and self-assembly of rMaSp1 were also analyzed.

CONCLUSION

This study successfully addressed key challenges in recombinant spidroin production by employing fusion tags (SUMO and self-shearing peptide intein) to enable the soluble expression of rMaSp1 and its dimer rMaSp1s-2Core. The secondary structure and self-assembly analyses further contributed to our understanding of recombinant spidroin. These findings enable the large-scale production of spidroin and its potential applications in the biomedical, chemical, and military industries, overcoming previous hurdles related to the solubility and toxicity associated with downstream processing.

Structure, production and application of spider silks

Spider silk plays a pivotal role in the diverse physiological activities of spiders, with its protein components exhibiting remarkable mechanical properties and biocompatibility. Spider silk proteins exhibit a high degree of repetitiveness, primarily constructed through the recurring arrangement of amino acid motifs, including (A)n, (GA)n, (GGX)n, and (GPGXX)n sequences. These repetitive sequences endow spider silk with different material properties. Recombinant spider silk proteins are produced through heterologous expression systems, and then spun into nanofibers using artificial spinning technology. These fibers have broad potential applications in the biomedical field, such as tissue engineering scaffolds, drug delivery carriers, sutures, and other biomaterials. However, enhancing the yield and performance of recombinant spider silk proteins, while facilitating large-scale production, continues to pose a significant challenge in the current landscape.

Recombinant production of spider silk protein in Physcomitrella photobioreactors

KEY MESSAGE

We report the successful moss-produced recombinant spider silk key protein component containing both the N- and the C-terminal domain. Spider dragline silk stands out as a remarkable biomaterial, representing one of nature's toughest fibres. Its strength rivals that of many synthetic fibres used commercially, rendering it applicable across various industrial and medical domains. However, its widespread utilisation requires cost-effective mass production. Biotechnology presents a promising avenue for achieving this goal, particularly through the production of recombinant dragline silk proteins in transgenic plant systems. This study aimed to assess the feasibility of producing one key protein component of dragline silk, MaSp1, from the western black widow spider, Latrodectus hesperus, the protein LhMaSp1, in the moss Physcomitrella (Physcomitrium patens). Here, we present the successful recombinant production of spider silk protein containing both the N- and C-terminal domains of LhMaSp1 in moss cells. The production of recombinant LhMaSp1 protein in Physcomitrella was performed in shake flasks and in five-litre photobioreactors and the correct synthesis of LhMaSp1 was proven via mass spectrometry. We estimate that the yield of recombinant spider silk protein in Physcomitrella bioreactors is above 0.82 mg/g fresh weight.

Non-invasive molecular species identification using spider silk proteomics

Accurate species identification is essential in biology, ecology, medicine, and agriculture, yet traditional methods relying on morphological characteristics often fail due to phenotypic plasticity and cryptic species. These limitations are particularly pronounced in small organisms with minimal distinguishing features. DNA barcoding has become a popular alternative; however, it requires invasive tissue sampling, making it unsuitable for delicate or rare organisms like insects and spiders. To address this challenge, we propose a non-invasive molecular method using proteomic analysis focused on species-specific protein sequences in spider silk, offering a viable solution for species identification without harming specimens. We developed a universal silk-dissolving method, followed by sequence similarity analysis to classify species into those identifiable at the species level and those distinguishable only to a group of closely related species. A bioinformatics pipeline was established to analyze peptide sequences, achieving 96% accuracy across 15 spider species, even in the presence of contaminants. This technique complements DNA barcoding and can be extended to other organisms producing biological materials. It holds promise in pest management, medical diagnostics, and improving public health by enabling accurate species identification without invasive procedures.

Native Silk Fibers: Protein Sequence and Structure Influences on Thermal and Mechanical Properties

Silk fibers produced by arthropods have inspired an array of materials with applications in healthcare, medical devices, textiles, and sustainability. Silks exhibit biodiversity with distinct variations in primary protein constituent sequences (fibroins, spidroins) and structures across taxonomic classifications, specifically the Lepidopteran and Araneae orders. Leveraging the biodiversity in arthropod silks offers advantages due to the diverse mechanical properties and thermal stabilities achievable, primarily attributed to variations in fiber crystallinity and repeating amino acid motifs. In this review, we aim to delineate known properties of silk fibers and correlate them with predicted protein sequences and secondary structures, informed by newly annotated genomes. We will discuss established patterns in repeat motifs governing specific properties and underscore the biological diversity within silk fibroin and spidroin sequences. Elucidating the relationship between protein sequences and properties of natural silk fibers will identify strategies for designing new materials through rational silk-based fiber design.

Characterization of the second type of tubuliform spidroin (TuSp1 variant 2) elucidates the essential role of cysteine within the repetitive domain in liquid-liquid phase separation-mediated silk formation and the mechanical properties of silk fibers

Orb-weaver spiders utilize morphologically differentiated abdominal glands to produce up to seven types of silks throughout their life cycles. Tubuliform silk is unique as it serves to protect developing embryos and hatchlings. However, our current understanding of the relationship between structure and function of tubuliform silk protein remains limited. Here, we present the full-length gene sequence of the second type of tubuliform spidroin (TuSp1 variant 2) from the orb-weaver spider Leucauge blanda. The L. blanda TuSp1 variant 2 (TuSp1-v2) contains 18 tandemly arrayed repeats, with each repeat having a cysteine residue. We demonstrate that the cysteine in L. blanda TuSp1-v2 repeats can form intermolecular disulfide bond and promote the liquid-liquid phase separation (LLPS) for silk formation. Moreover, the presence of cysteine partially enhances the thermostability of soluble spidroins and the mechanical properties of fibers, as demonstrated by comparative analyses of miniature TuSp1-v2 and its mutants. The integration of mechanical and structural data indicates that the recombinant TuSp1-v2 fiber exhibits high UV-A stability in both its mechanical and structural properties. This study provides new insights into the functions of cysteine in repetitive region and implies promising potentials for development new spidroin-based biomaterials.

Mechanical and structural features of three AcSp proteins underlie the diverse material properties of aciniform silks of Neoscona spiders

Spider silks are desirable multicomponent biomaterials characterized by great tensile strength, extensibility, and biocompatibility. Of all spider silk types, aciniform silk has highest toughness due to its combination of high tensile strength and elsticity. Here, we identify three major spidroin components (AcSp1A, AcSp1B, and AcSp2) from aciniform silk of orbweb weaving spider, Neoscona scylloides, and present their full-length coding gene sequences. Comparative sequence and expression level analysis show that AcSp1B has highest expression level and higher serine content than other two AcSp proteins, while the AcSp2 shows very low mRNA level. Furthermore, three recombinant minimalist AcSp proteins are produced and could be induced to form fibers by shear forces in a physiological buffer. The manual-drawn AcSp1B fiber shows strongest tensile strength among three AcSp fibers because of its higher β-sheet formed by abundant serine content. We also compare mechanical properties of aciniform silks between two Neoscona species (N. theisi and N. scylloides) and found that aciniform silks from N. theisi exhibit higher tensile strength than those of N. scylloides, which may result from altering expression levels of two AcSp1 proteins. Collectively, our results provide insights into the mechanical features of each component in aciniform silk from N. scylloides and reveal the molecular mechanism of diverse material properties of aciniform silk among species.

Correlating Mechanical Properties and Sequence Motifs in Artificial Spider Silk by Targeted Motif Substitution

The major ampullate silk of orb-weaving spiders is renowned for its exceptional mechanical properties, including high tensile strength and extensibility. The development of artificial spider silk presents a promising alternative to traditional fibers with significant environmental impacts. This study aims to elucidate the relationship between sequence motifs of natural spider silk and the mechanical properties of artificial spider silk. Using the Spider Silkome Database, we identified motifs correlated with specific physical properties and substituted them into MaSp2-based mini-spidroin BP1. We then measured the mechanical properties of the resulting recombinant artificial spider silk through tensile tests, observed structural properties via birefringence measurement and wide-angle X-ray scattering, and evaluated the water response through boiled water shrinkage tests. Introducing a positively correlated motif increased the tensile strength by 9.3%, while a negatively correlated motif decreased it by 5.1%, confirming the sequence-property relationship. These findings demonstrate that targeted motif substitution can effectively control the physical properties of artificial spider silk, facilitating the development of sustainable biomaterials with tailored mechanical properties for diverse industrial applications.

Synthesis and In Situ Thermal Induction of β-Sheet Nanocrystals in Spider Silk-Inspired Copolypeptides

Spider silk, known for its exceptional tensile strength, extensibility, and toughness, continues to inspire advancements in polymer and materials science. Despite extensive research, synthesizing materials that encompass all these properties remains a significant challenge. This study addresses this challenge by developing high molecular-weight multiblock synthetic copolypeptides that mimic the hierarchical structure and mechanical properties of spider silk. Using autoaccelerated ring-opening polymerization of N-carboxyanhydrides, we synthesized copolypeptides featuring transformable β-sheet blocks. These blocks retain a helical structure during synthesis but transition into β-sheet nanocrystals in situ during solvent-free thermal mechanical processing. Compression molding was employed to induce hierarchical ordering within the copolypeptide films, resulting in a solid "liquid crystalline" structure that undergoes a temperature-induced α-to-β structural transformation. This transformation integrates β-sheet nanocrystals throughout the helical block matrix, significantly enhancing the material's mechanical performance. Our innovative synthesis and processing strategy, which involves alternating sequences of α-helical and β-sheet blocks with various β-sheet-forming NCAs, enables the customization of diverse mechanical characteristics. These advancements not only deepen our understanding of the fundamental design principles of spider silk but also pave the way for a new generation of high-performance, silk-inspired synthetic copolypeptides with broad application potential.

Effects of Mini-Spidroin Repeat Region on the Mechanical Properties of Artificial Spider Silk Fibers

Spiders can produce up to seven different types of silk, each with unique mechanical properties that stem from variations in the repetitive regions of spider silk proteins (spidroins). Artificial spider silk can be made from mini-spidroins in an all-aqueous-based spinning process, but the strongest fibers seldom reach more than 25% of the strength of native silk fibers. With the aim to improve the mechanical properties of silk fibers made from mini-spidroins and to understand the relationship between the protein design and the mechanical properties of the fibers, we designed 16 new spidroins, ranging from 31.7 to 59.5 kDa, that feature the globular spidroin N- and C-terminal domains, but harbor different repetitive sequences. We found that more than 50% of these constructs could be spun by extruding them into low-pH aqueous buffer and that the best fibers were produced from proteins whose repeat regions were derived from major ampullate spidroin 4 (MaSp4) and elastin. The mechanical properties differed between fiber types but did not correlate with the expected properties based on the origin of the repeats, suggesting that additional factors beyond protein design impact the properties of the fibers.

Disentangling the Web: An Interdisciplinary Review on the Potential and Feasibility of Spider Silk Bioproduction

The remarkable material properties of spider silk, such as its high toughness and tensile strength combined with its low density, make it a highly sought-after material with myriad applications. In addition, the biological nature of spider silk makes it a promising, potentially sustainable alternative to many toxic or petrochemical-derived materials. Therefore, interest in the heterologous production of spider silk proteins has greatly increased over the past few decades, making recombinant spider silk an important frontier in biomanufacturing. This has resulted in a diversity of potential host organisms, a large space for sequence design, and a variety of downstream processing techniques and product applications for spider silk production. Here, we highlight advances in each of these technical aspects as well as white spaces therein, still ripe for further investigation and discovery. Additionally, industry landscaping, patent analyses, and interviews with Key Opinion Leaders help define both the research and industry landscapes. In particular, we found that though textiles dominated the early products proposed by companies, the versatile nature of spider silk has opened up possibilities in other industries, such as high-performance materials in automotive applications or biomedical therapies. While continuing enthusiasm has imbued scientists and investors alike, many technical and business considerations still remain unsolved before spider silk can be democratized as a high-performance product. We provide insights and strategies for overcoming these initial hurdles, and we highlight the importance of collaboration between academia, industry, and policy makers. Linking technical considerations to business and market entry strategies highlights the importance of a holistic approach for the effective scale-up and commercial viability of spider silk bioproduction.

Strategies for Making High-Performance Artificial Spider Silk Fibers

Artificial spider silk is an attractive material for many technical applications since it is a biobased fiber that can be produced under ambient conditions but still outcompetes synthetic fibers (e.g., Kevlar) in terms of toughness. Industrial use of this material requires bulk-scale production of recombinant spider silk proteins in heterologous host and replication of the pristine fiber's mechanical properties. High molecular weight spider silk proteins can be spun into fibers with impressive mechanical properties, but the production levels are too low to allow commercialization of the material. Small spider silk proteins, on the other hand, can be produced at yields that are compatible with industrial use, but the mechanical properties of such fibers need to be improved. Here, the literature on wet-spinning of artificial spider silk fibers is summarized and analyzed with a focus on mechanical performance. Furthermore, several strategies for how to improve the properties of such fibers, including optimized protein composition, smarter spinning setups, innovative protein engineering, chemical and physical crosslinking as well as the incorporation of nanomaterials in composite fibers, are outlined and discussed.

Nanoassembly of spider silk protein mediated by intrinsically disordered regions

Spider silk is the self-assembling product of silk proteins each containing multiple repeating units. Each repeating unit is entirely intrinsically disordered or contains a small disordered domain. The role of the disordered domain/unit in conferring silk protein storage and self-assembly is not fully understood yet. Here, we used biophysical and biochemical techniques to investigate the self-assembly of a miniature version of a minor ampullate spidroin (denoted as miniMiSp). miniMiSp consists of two identical intrinsically disordered domains, one folded repetitive domain, and two folded terminal domains. Our data indicated that miniMiSp self-assembles into oligomers and further into liquid droplets. The oligomerization is attributed to the aggregation-prone property of both the disordered domains and the folded repetitive domain. Our results support the model of micellar structure for silk proteins at high protein concentrations. The disordered domain is indispensable for liquid droplet formation via liquid-liquid phase separation, and tyrosine residues located in the disordered domain make dominant contributions to stability of the liquid droplets. As the same tyrosine residues are also critical to fibrillation, the liquid droplets are likely an intermediate state between the solution state and the fiber state. Additionally, the terminal domains contribute to the pH- and salt-dependent self-assembly properties.

Insight into the adaptive role of arachnid genome-wide duplication through chromosome-level genome assembly of the Western black widow spider

Although spiders are one of the most diverse groups of arthropods, the genetic architecture of their evolutionary adaptations is largely unknown. Specifically, ancient genome-wide duplication occurring during arachnid evolution ~450 mya resulted in a vast assembly of gene families, yet the extent to which selection has shaped this variation is understudied. To aid in comparative genome sequence analyses, we provide a chromosome-level genome of the Western black widow spider (Latrodectus hesperus)-a focus due to its silk properties, venom applications, and as a model for urban adaptation. We used long-read and Hi-C sequencing data, combined with transcriptomes, to assemble 14 chromosomes in a 1.46 Gb genome, with 38,393 genes annotated, and a BUSCO score of 95.3%. Our analyses identified high repetitive gene content and heterozygosity, consistent with other spider genomes, which has led to challenges in genome characterization. Our comparative evolutionary analyses of eight genomes available for species within the Araneoidea group (orb weavers and their descendants) identified 1,827 single-copy orthologs. Of these, 155 exhibit significant positive selection primarily associated with developmental genes, and with traits linked to sensory perception. These results support the hypothesis that several traits unique to spiders emerged from the adaptive evolution of ohnologs-or retained ancestrally duplicated genes-from ancient genome-wide duplication. These comparative spider genome analyses can serve as a model to understand how positive selection continually shapes ancestral duplications in generating novel traits today within and between diverse taxonomic groups.

Special Prey, Special Glue: NMR Spectroscopy on Aggregate Glue Components of Moth-Specialist Spiders, Cyrtarachninae

Orb-weaver spiders produce upwards of seven different types of silk, each with unique material properties. We focus on the adhesive within orb-weaving spider webs, aggregate glue silk. These droplets are composed of three main components: water, glycoproteins, and a wide range of low molecular mass compounds (LMMCs). These LMMCs are known to play a crucial role in maintaining the material properties of the glycoproteins, aid in water absorption from the environment, and increase surface adhesion. Orb-weavers within the Cyrtarachninae subfamily are moth specialists and have evolved glue droplets with novel material properties. This study investigated the biochemical composition and diversity of the LMMCs present in the aggregate glue of eight moth-specialist species and compared them with five generalist orb-weavers using nuclear magnetic resonance (NMR) spectroscopy. We hypothesized that the novel drying ability of moth-specialist glue was accompanied by novel LMMCs and lower overall percentages by silk weight of LMMCs. We measured no difference in LMMC weight by the type of prey specialization, but observed novel compositions in the glue of all eight moth-catching species. Further, we quantified the presence of a previously reported but unidentified compound that appears in the glue of all moth specialists. These silks can provide insight into the functions of bioadhesives and inform our own synthetic adhesives.

Influence of Spider Silk Protein Structure on Mechanical and Biological Properties for Energetic Material Detection

Spider silk protein, renowned for its excellent mechanical properties, biodegradability, chemical stability, and low immune and inflammatory response activation, consists of a core domain with a repeat sequence and non-repeating sequences at the N-terminal and C-terminal. In this review, we focus on the relationship between the silk structure and its mechanical properties, exploring the potential applications of spider silk materials in the detection of energetic materials.

Rapid production of chimeric silkworm/spider silk with improved mechanical properties by infection of nonpermissive Bombyx mori with recombinant AcMNPV harboring native-size of spidroin genes

Spider silks with excellent mechanical properties attract more attention from scientists worldwide, and the dragline silk that serves as the framework of the spider's web is considered one of the strongest fibers. However, it is unfeasible for large-scale production of spider silk due to its highly territorial, cannibalistic, predatory, and solitary behavior. Herein, to alleviate some of these problems and explore aneasy way to produce spider fibers, we constructed recombinant baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) simultaneously expressing Trichonephila clavipes native ampullate spidroin 2 (MaSp-G) and spidroin 1 (MaSp-C) driven by the promoters of silkworm fibroin genes, to infect the nonpermissive Bombyx mori larvae at the fifth instar. MaSp-G and MaSp-C were co-expressed in the posterior silk glands (PSGs) of infected silkworms and successfully secreted into the lumen of the silk gland for fibroin globule assembly. The integration of MaSp-G and MaSp-C into silkworm silk fibers significantly improved the mechanical properties of these chimeric silk fibers, especially the strength and extensibility, which may be caused by the increment of β-sheet in the chimeric silkworm/spider silk fiber. These results demonstrated that silkworms could be developed as the nonpermissive heterologous host for the mass production of chimeric silkworm/spider silk fibers via the recombinant baculovirus AcMNPV.

NMR assignment and dynamics of the dimeric form of soluble C-terminal domain major ampullate spidroin 2 from Latrodectus hesperus

Spider dragline silk has attracted great interest due to its outstanding mechanical properties, which exceed those of man-made synthetic materials. Dragline silk, which is composed of at least major ampullate spider silk protein 1 and 2 (MaSp1 and MaSp2), contains a long repetitive domain flanked by N-terminal and C-terminal domains (NTD and CTD). Despite the small size of the CTD, this domain plays a crucial role as a molecular switch that regulates and directs spider silk self-assembly. In this study, we report the 1H, 13C, and 15N chemical shift assignments of the Latrodectus hesperus MaSp2 CTD in dimeric form at pH 7. Our solution NMR data demonstrated that this protein contains five helix regions connected by a flexible linker.

A Minispidroin Guides the Molecular Design for Cellular Condensation Mechanisms in S. cerevisiae

Structural engineering of molecules for condensation is an emerging technique within synthetic biology. Liquid-liquid phase separation of biomolecules leading to condensation is a central step in the assembly of biological materials into their functional forms. Intracellular condensates can also function within cells in a regulatory manner to facilitate reaction pathways and to compartmentalize interactions. We need to develop a strong understanding of how to design molecules for condensates and how their in vivo-in vitro properties are related. The spider silk protein NT2RepCT undergoes condensation during its fiber-forming process. Using parallel in vivo and in vitro characterization, in this study, we mapped the effects of intracellular conditions for NT2RepCT and its several structural variants. We found that intracellular conditions may suppress to some extent condensation whereas molecular crowding affects both condensate properties and their formation. Intracellular characterization of protein condensation allowed experiments on pH effects and solubilization to be performed within yeast cells. The growth of intracellular NT2RepCT condensates was restricted, and Ostwald ripening was not observed in yeast cells, in contrast to earlier observations in E. coli. Our results lead the way to using intracellular condensation to screen for properties of molecular assembly. For characterizing different structural variants, intracellular functional characterization can eliminate the need for time-consuming batch purification and in vitro condensation. Therefore, we suggest that the in vivo-in vitro understanding will become useful in, e.g., high-throughput screening for molecular functions and in strategies for designing tunable intracellular condensates.

Memory effect of spider major ampullate silk in loading-unloading cycles and the structural connotations

Spider silk is repeatedly stretched while performing biological functions. There is a close relationship between the shape change of the fibre materials and their mechanical properties. However, the effect of the deformation and interval time on the structure and tensile behaviour properties of spider silk after repeatedly stretching by given strain value has been rarely reported. Here we found that major ampullate silk (MAS) can revert its tensile behaviour independent of its previous loading history via intervals of approximately 8 s to 5 min with constant and increased elongation, respectively, after being subjected to yield and hardening regions. The true stress-true strain curve beyond a given value of true strain is independent from the previous loading history of the sample. Even after longer intervals (≥1 h), MAS can reproduce the last tensile behaviour via one stretched. Despite recognizing the development of irreversible deformations in the material when tested in air, the reversible change in tensile behaviour outside the spider silk's elastic region has rarely been observed before. MAS has at least one proper ground state that allows it to present good shape and mechanical behaviour memory in terms of longitudinal stretching, functioning as a new strategy to achieve certain tensile properties. The analysis of the true stress-true strain curves was performed from a series of loading‒unloading tests to evaluate the evolution of those mechanical parameters with the cycle number. The elastic modulus measured in the loading steps increases monotonously with increasing values of true strain reached in the cycles. In contrast, a marginal variation is found in the values of the yield stress measured in the different cycles. The memory and variation in the mechanical behaviour and performance of MAS can be accounted for through the irreversible and reversible deformation micromechanisms and its combination in which the viscoelasticity of the material plays a leading role. These findings may be helpful to guide the biomimetic design of novel fibre materials such as spider silk gut via artificially stretching spider silk glands.

A brief review on the mechanisms and approaches of silk spinning-inspired biofabrication

Silk spinning, observed in spiders and insects, exhibits a remarkable biological source of inspiration for advanced polymer fabrications. Because of the systems design, silk spinning represents a holistic and circular approach to sustainable polymer fabrication, characterized by renewable resources, ambient and aqueous processing conditions, and fully recyclable "wastes." Also, silk spinning results in structures that are characterized by the combination of monolithic proteinaceous composition and mechanical strength, as well as demonstrate tunable degradation profiles and minimal immunogenicity, thus making it a viable alternative to most synthetic polymers for the development of advanced biomedical devices. However, the fundamental mechanisms of silk spinning remain incompletely understood, thus impeding the efforts to harness the advantageous properties of silk spinning. Here, we present a concise and timely review of several essential features of silk spinning, including the molecular designs of silk proteins and the solvent cues along the spinning apparatus. The solvent cues, including salt ions, pH, and water content, are suggested to direct the hierarchical assembly of silk proteins and thus play a central role in silk spinning. We also discuss several hypotheses on the roles of solvent cues to provide a relatively comprehensive analysis and to identify the current knowledge gap. We then review the state-of-the-art bioinspired fabrications with silk proteins, including fiber spinning and additive approaches/three-dimensional (3D) printing. An emphasis throughout the article is placed on the universal characteristics of silk spinning developed through millions of years of individual evolution pathways in spiders and silkworms. This review serves as a stepping stone for future research endeavors, facilitating the in vitro recapitulation of silk spinning and advancing the field of bioinspired polymer fabrication.

Lampshade web spider Ectatosticta davidi chromosome-level genome assembly provides evidence for its phylogenetic position

The spider of Ectatosticta davidi, belonging to the lamp-shade web spider family, Hypochilidae, which is closely related to Hypochilidae and Filistatidae and recovered as sister of the rest Araneomorphs spiders. Here we show the final assembled genome of E. davidi with 2.16 Gb in 15 chromosomes. Then we confirm the evolutionary position of Hypochilidae. Moreover, we find that the GMC gene family exhibit high conservation throughout the evolution of true spiders. We also find that the MaSp genes of E. davidi may represent an early stage of MaSp and MiSp genes in other true spiders, while CrSp shares a common origin with AgSp and PySp but differ from MaSp. Altogether, this study contributes to addressing the limited availability of genomic sequences from Hypochilidae spiders, and provides a valuable resource for investigating the genomic evolution of spiders.

pH-dependent self-assembly mechanism of a single repetitive domain from a spider silk protein

Spider silk is self-assembled from full-length silk proteins, and some silk protein fragments can also form silk-like fibers in vitro. However, the mechanism underlying the silk fiber formation is not understood well. In this study, we investigated the fiber formation of a single repetitive domain (RP) from a minor ampullate silk protein (MiSp). Our findings revealed that pH and salt concentration affect not only the stability of MiSp-RP but also its self-assembly into fibers and aggregates. Using nuclear magnetic resonance (NMR) spectroscopy, we solved the three-dimensional (3D) structure of MiSp RP in aqueous solution. On the basis of the structure and mutagenesis, we revealed that charge-dipole interactions are responsible for the pH- and salt-dependent properties of MiSp-RP. Our results indicate that fiber formation is regulated by a delicate balance between intermolecular and intramolecular interactions, rather than by the protein stability alone. These findings have implications for the design of silk proteins for mass production of spider silk.

Compensatory relationship between low-complexity regions and gene paralogy in the evolution of prokaryotes

The evolution of genomes in all life forms involves two distinct, dynamic types of genomic changes: gene duplication (and loss) that shape families of paralogous genes and extension (and contraction) of low-complexity regions (LCR), which occurs through dynamics of short repeats in protein-coding genes. Although the roles of each of these types of events in genome evolution have been studied, their co-evolutionary dynamics is not thoroughly understood. Here, by analyzing a wide range of genomes from diverse bacteria and archaea, we show that LCR and paralogy represent two distinct routes of evolution that are inversely correlated. The emergence of LCR is a prominent evolutionary mechanism in fast evolving, young protein families, whereas paralogy dominates the comparatively slow evolution of old protein families. The analysis of multiple prokaryotic genomes shows that the formation of LCR is likely a widespread, transient evolutionary mechanism that temporally and locally affects also ancestral functions, but apparently, fades away with time, under mutational and selective pressures, yielding to gene paralogy. We propose that compensatory relationships between short-term and longer-term evolutionary mechanisms are universal in the evolution of life.

Variation in the Elastic Modulus and Increased Energy Dissipation Induced by Cyclic Straining of Argiope bruennichi Major Ampullate Gland Silk

The trends exhibited by the parameters that describe the mechanical behaviour of major ampullate gland silk fibers spun by Argiope bruennichi spiders is explored by performing a series of loading-unloading tests at increasing values of strain, and by the subsequent analysis of the true stress-true strain curves obtained from these cycles. The elastic modulus, yields stress, energy absorbed, and energy dissipated in each cycle are computed in order to evaluate the evolution of these mechanical parameters with this cyclic straining. The elastic modulus is observed to increase steadily under these loading conditions, while only a moderate variation is found in the yield stress. It is also observed that a significant proportion of the energy initially absorbed in each cycle is not only dissipated, but that the material may recover partially from the associated irreversible deformation. This variation in the mechanical performance of spider silk is accounted for through a combination of irreversible and reversible deformation micromechanisms in which the viscoelasticity of the material plays a leading role.

Silk fibroin production in Escherichia coli is limited by a positive feedback loop between metabolic burden and toxicity stress

To investigate the metabolic elasticity and production bottlenecks for recombinant silk proteins in Escherichia coli, we performed a comprehensive characterization of one elastin-like peptide strain (ELP) and two silk protein strains (A5 4mer, A5 16mer). Our approach included ¹³C metabolic flux analysis, genome-scale modeling, transcription analysis, and ¹³C-assisted media optimization experiments. Three engineered strains maintained their central flux network during growth, while measurable metabolic flux redistributions (such as the Entner-Doudoroff pathway) were detected. Under metabolic burdens, the reduced TCA fluxes forced the engineered strain to rely more on substrate-level phosphorylation for ATP production, which increased acetate overflow. Acetate (as low as 10 mM) in the media was highly toxic to silk-producing strains, which reduced 4mer production by 43% and 16mer by 84%, respectively. Due to the high toxicity of large-size silk proteins, 16mer's productivity was limited, particularly in the minimal medium. Therefore, metabolic burden, overflow acetate, and toxicity of silk proteins may form a vicious positive feedback loop that fractures the metabolic network. Three solutions could be applied: 1) addition of building block supplements (i.e., eight key amino acids: His, Ile, Phe, Pro, Tyr, Lys, Met, Glu) to reduce metabolic burden; 2) disengagement of growth and production; and 3) use of non-glucose based substrate to reduce acetate overflow. Other reported strategies were also discussed in light of decoupling this positive feedback loop.

Predicting mechanical properties of silk from its amino acid sequences via machine learning

The silk fiber is increasingly being sought for its superior mechanical properties, biocompatibility, and eco-friendliness, making it promising as a base material for various applications. One of the characteristics of protein fibers, such as silk, is that their mechanical properties are significantly dependent on the amino acid sequence. Numerous studies have been conducted to determine the specific relationship between the amino acid sequence of silk and its mechanical properties. Still, the relationship between the amino acid sequence of silk and its mechanical properties is yet to be clarified. Other fields have adopted machine learning (ML) to establish a relationship between the inputs, such as the ratio of different input material compositions and the resulting mechanical properties. We have proposed a method to convert the amino acid sequence into numerical values for input and succeeded in predicting the mechanical properties of silk from its amino acid sequences. Our study sheds light on predicting mechanical properties of silk fiber from respective amino acid sequences.

Biomimetic natural biomaterials for tissue engineering and regenerative medicine: new biosynthesis methods, recent advances, and emerging applications

Biomimetic materials have emerged as attractive and competitive alternatives for tissue engineering (TE) and regenerative medicine. In contrast to conventional biomaterials or synthetic materials, biomimetic scaffolds based on natural biomaterial can offer cells a broad spectrum of biochemical and biophysical cues that mimic the in vivo extracellular matrix (ECM). Additionally, such materials have mechanical adaptability, microstructure interconnectivity, and inherent bioactivity, making them ideal for the design of living implants for specific applications in TE and regenerative medicine. This paper provides an overview for recent progress of biomimetic natural biomaterials (BNBMs), including advances in their preparation, functionality, potential applications and future challenges. We highlight recent advances in the fabrication of BNBMs and outline general strategies for functionalizing and tailoring the BNBMs with various biological and physicochemical characteristics of native ECM. Moreover, we offer an overview of recent key advances in the functionalization and applications of versatile BNBMs for TE applications. Finally, we conclude by offering our perspective on open challenges and future developments in this rapidly-evolving field.

A molecular atlas reveals the tri-sectional spinning mechanism of spider dragline silk

The process of natural silk production in the spider major ampullate (Ma) gland endows dragline silk with extraordinary mechanical properties and the potential for biomimetic applications. However, the precise genetic roles of the Ma gland during this process remain unknown. Here, we performed a systematic molecular atlas of dragline silk production through a high-quality genome assembly for the golden orb-weaving spider Trichonephila clavata and a multiomics approach to defining the Ma gland tri-sectional architecture: Tail, Sac, and Duct. We uncovered a hierarchical biosynthesis of spidroins, organic acids, lipids, and chitin in the sectionalized Ma gland dedicated to fine silk constitution. The ordered secretion of spidroins was achieved by the synergetic regulation of epigenetic and ceRNA signatures for genomic group-distributed spidroin genes. Single-cellular and spatial RNA profiling identified ten cell types with partitioned functional division determining the tri-sectional organization of the Ma gland. Convergence analysis and genetic manipulation further validated that this tri-sectional architecture of the silk gland was analogous across Arthropoda and inextricably linked with silk formation. Collectively, our study provides multidimensional data that significantly expand the knowledge of spider dragline silk generation and ultimately benefit innovation in spider-inspired fibers.

Novel insights into construct toxicity, strain optimization, and primary sequence design for producing recombinant silk fibroin and elastin-like peptide in E. coli

Spider silk proteins (spidroins) are a remarkable class of biomaterials that exhibit a unique combination of high-value attributes and can be processed into numerous morphologies for targeted applications in diverse fields. Recombinant production of spidroins represents the most promising route towards establishing the industrial production of the material, however, recombinant spider silk production suffers from fundamental difficulties that includes low titers, plasmid instability, and translational inefficiencies. In this work, we sought to gain a deeper understanding of upstream bottlenecks that exist in the field through the production of a panel of systematically varied spidroin sequences in multiple E. coli strains. A restriction on basal expression and specific genetic mutations related to stress responses were identified as primary factors that facilitated higher titers of the recombinant silk constructs. Using these findings, a novel strain of E. coli was created that produces recombinant silk constructs at levels 4-33 times higher than standard BL21(DE3). However, these findings did not extend to a similar recombinant protein, an elastin-like peptide. It was found that the recombinant silk proteins, but not the elastin-like peptide, exert toxicity on the E. coli host system, possibly through their high degree of intrinsic disorder. Along with strain engineering, a bioprocess design that utilizes longer culturing times and attenuated induction was found to raise recombinant silk titers by seven-fold and mitigate toxicity. Targeted alteration to the primary sequence of the recombinant silk constructs was also found to mitigate toxicity. These findings identify multiple points of focus for future work seeking to further optimize the recombinant production of silk proteins and is the first work to identify the intrinsic disorder and subsequent toxicity of certain spidroin constructs as a primary factor related to the difficulties of production.

Chromosome-level genome and the identification of sex chromosomes in Uloborus diversus

The orb web is a remarkable example of animal architecture that is observed in families of spiders that diverged over 200 million years ago. While several genomes exist for araneid orb-weavers, none exist for other orb-weaving families, hampering efforts to investigate the genetic basis of this complex behavior. Here we present a chromosome-level genome assembly for the cribellate orb-weaving spider Uloborus diversus. The assembly reinforces evidence of an ancient arachnid genome duplication and identifies complete open reading frames for every class of spidroin gene, which encode the proteins that are the key structural components of spider silks. We identified the 2 X chromosomes for U. diversus and identify candidate sex-determining loci. This chromosome-level assembly will be a valuable resource for evolutionary research into the origins of orb-weaving, spidroin evolution, chromosomal rearrangement, and chromosomal sex determination in spiders.

Massive production of fibroin nano-fibrous biomaterial by turbulent co-flow

Among the different polymers (proteins, polysaccharides, etc.) that make up natural fibers, fibroin is a protein produced by silk spinning animals, which have developed an optimized system for the conversion of a highly concentrated solution of this protein into high-performance solid fibers. This protein undergoes a self-assembly process in the silk glands that result from chemical gradients and by the application of mechanical stresses during the last step of the process. In the quest for a process that could mimic natural spinning at massive scales, we have discovered that turbulence offers a novel and promising solution: a turbulent liquid jet can be formed by a chemically green and simple coagulating liquid (a diluted solution of acetic acid in etanol) co-flowing with a concentrated solution of fibroin in water by the use of a Flow Blurring nebulizer. In this system, (a) the co-flowing coagulant liquid extracts water from the original protein solution and, simultaneously, (b) the self-assembled proteins are subjected to mechanical actions, including splitting and stretching. Given the non-negligible produced content with the size and appearance of natural silk, the stochastic distribution of those effects in our process should contain the range of natural ones found in animals. The resulting easily functionalizable and tunable one-step material is 100% biocompatible, and our method a perfect candidate to large-scale, low-cost, green and sustainable processing of fibroin for fibres and textiles.

Rapid molecular diversification and homogenization of clustered major ampullate silk genes in Argiope garden spiders

The evolutionary diversification of orb-web weaving spiders is closely tied to the mechanical performance of dragline silk. This proteinaceous fiber provides the primary structural framework of orb web architecture, and its extraordinary toughness allows these structures to absorb the high energy of aerial prey impact. The dominant model of dragline silk molecular structure involves the combined function of two highly repetitive, spider-specific, silk genes (spidroins)-MaSp1 and MaSp2. Recent genomic studies, however, have suggested this framework is overly simplistic, and our understanding of how MaSp genes evolve is limited. Here we present a comprehensive analysis of MaSp structural and evolutionary diversity across species of Argiope (garden spiders). This genomic analysis reveals the largest catalog of MaSp genes found in any spider, driven largely by an expansion of MaSp2 genes. The rapid diversification of Argiope MaSp genes, located primarily in a single genomic cluster, is associated with profound changes in silk gene structure. MaSp2 genes, in particular, have evolved complex hierarchically organized repeat units (ensemble repeats) delineated by novel introns that exhibit remarkable evolutionary dynamics. These repetitive introns have arisen independently within the genus, are highly homogenized within a gene, but diverge rapidly between genes. In some cases, these iterated introns are organized in an alternating structure in which every other intron is nearly identical in sequence. We hypothesize that this intron structure has evolved to facilitate homogenization of the coding sequence. We also find evidence of intergenic gene conversion and identify a more diverse array of stereotypical amino acid repeats than previously recognized. Overall, the extreme diversification found among MaSp genes requires changes in the structure-function model of dragline silk performance that focuses on the differential use and interaction among various MaSp paralogs as well as the impact of ensemble repeat structure and different amino acid motifs on mechanical behavior.

Differences in the Elastomeric Behavior of Polyglycine-Rich Regions of Spidroin 1 and 2 Proteins

Two different polyglycine-rich fragments were selected as representatives of major ampullate gland spidroins (MaSp) 1 and 2 types, and their behavior in a water-saturated environment was simulated within the framework of molecular dynamics (MD). The selected fragments are found in the sequences of the proteins MaSp1a and MaSp2.2a of Argiope aurantia with respective lengths of 36 amino acids (MaSp1a) and 50 amino acids (MaSp2.2s). The simulation took the fully extended β-pleated conformation as reference, and MD was used to determine the equilibrium configuration in the absence of external forces. Subsequently, MD were employed to calculate the variation in the distance between the ends of the fragments when subjected to an increasing force. Both fragments show an elastomeric behavior that can be modeled as a freely jointed chain with links of comparable length, and a larger number of links in the spidroin 2 fragment. It is found, however, that the maximum recovery force recorded from the spidroin 2 peptide (F_max ≈ 400 pN) is found to be significantly larger than that of the spidroin 1 (F_max ≈ 250 pN). The increase in the recovery force of the spidroin 2 polyglycine-rich fragment may be correlated with the larger values observed in the strain at breaking of major ampullate silk fibers spun by Araneoidea species, which contain spidroin 2 proteins, compared to the material produced by spider species that lack these spidroins (RTA-clade).

1000 spider silkomes: Linking sequences to silk physical properties

Spider silks are among the toughest known materials and thus provide models for renewable, biodegradable, and sustainable biopolymers. However, the entirety of their diversity still remains elusive, and silks that exceed the performance limits of industrial fibers are constantly being found. We obtained transcriptome assemblies from 1098 species of spiders to comprehensively catalog silk gene sequences and measured the mechanical, thermal, structural, and hydration properties of the dragline silks of 446 species. The combination of these silk protein genotype-phenotype data revealed essential contributions of multicomponent structures with major ampullate spidroin 1 to 3 paralogs in high-performance dragline silks and numerous amino acid motifs contributing to each of the measured properties. We hope that our global sampling, comprehensive testing, integrated analysis, and open data will provide a solid starting point for future biomaterial designs.

Bioengineering of spider silks for the production of biomedical materials

Spider silks are well known for their extraordinary mechanical properties. This characteristic is a result of the interplay of composition, structure and self-assembly of spider silk proteins (spidroins). Advances in synthetic biology have enabled the design and production of spidroins with the aim of biomimicking the structure-property-function relationships of spider silks. Although in nature only fibers are formed from spidroins, in vitro, scientists can explore non-natural morphologies including nanofibrils, particles, capsules, hydrogels, films or foams. The versatility of spidroins, along with their biocompatible and biodegradable nature, also placed them as leading-edge biological macromolecules for improved drug delivery and various biomedical applications. Accordingly, in this review, we highlight the relationship between the molecular structure of spider silk and its mechanical properties and aims to provide a critical summary of recent progress in research employing recombinantly produced bioengineered spidroins for the production of innovative bio-derived structural materials.

Molecular Insights into the Self-Assembly of Block Copolymer Suckerin Polypeptides into Nanoconfined β-Sheets

Suckerin in squid sucker ring teeth is a block-copolymer peptide comprised of two repeating modules-the alanine and histidine-rich M1 and the glycine-rich M2. Suckerin self-assemblies display excellent thermo-plasticity and pH-responsive properties, along with the high biocompatibility, biodegradability, and sustainability. However, the self-assembly mechanism and the detailed role of each module are still elusive, limiting the capability of applying and manipulating such biomaterials. Here, the self-assembly dynamics of the two modules and two minimalist suckerin-mimetic block-copolymers, M1-M2-M1 and M2-M1-M2, in silico is investigated. The simulation results demonstrate that M2 has a stronger self-association but weaker β-sheet propensities than M1. The high self-assembly propensity of M2 allows the minimalist block-copolymer peptides to coalesce with microphase separation, enabling the formation of nanoconfined β-sheets in the matrix formed by M1-M2 contacts. Since these glycine-rich fragments with scatted hydrophobic and aromatic residues are building blocks of many other block-copolymer peptides, the study suggests that these modules function as the "molecular glue" in addition to the flexible linker or spacer to drive the self-assembly and microphase separation. The uncovered molecular insights may help understand the structure and function of suckerin and also aid in the design of functional block-copolymer peptides for nanotechnology and biomedicine applications.

Characterization of two full-length Araneus ventricosus major ampullate silk protein genes

Major ampullate silk is noted for its great tensile strength and extensibility. The impressive material properties of major ampullate silk result from their component proteins that encoded by members of the spidroin (spider fibroin) gene family. Although the major ampullate spidroin type has evolved multiple variants within specific-species, most sequences are fragmented. Here, we present two complete major ampullate spidroin genes from the orb-weaving spider Araneus ventricosus. Due to the abundant GPG motifs in their repetitive region, the two MaSp genes were grouped in MaSp2 subclass and named MaSp2C and MaSp2D, respectively. Analysis of the full-length gene sequences reveals that both of them include a single enormous exon (10,851 bp for MaSp2C and 8640 bp for MaSp2D) that mainly translates into a central repetitive region containing multiple amino acid motifs that can be organized into five ensemble types. We use gene-specific PCR primers to search the cDNA from major ampullate glands and find evidence for alternative splicing of MaSp2D transcripts into a minor spliceoform lacking the entire repetitive domain as well as the partial terminal regions. Our results not only provide new templates for protein-based materials with tailored properties, but suggest gene and transcriptional diversity of major ampullate silk.

Protein secondary structure in spider silk nanofibrils

Nanofibrils play a pivotal role in spider silk and are responsible for many of the impressive properties of this unique natural material. However, little is known about the internal structure of these protein fibrils. We carry out polarized Raman and polarized Fourier-transform infrared spectroscopies on native spider silk nanofibrils and determine the concentrations of six distinct protein secondary structures, including β-sheets, and two types of helical structures, for which we also determine orientation distributions. Our advancements in peak assignments are in full agreement with the published silk vibrational spectroscopy literature. We further corroborate our findings with X-ray diffraction and magic-angle spinning nuclear magnetic resonance experiments. Based on the latter and on polypeptide Raman spectra, we assess the role of key amino acids in different secondary structures. For the recluse spider we develop a highly detailed structural model, featuring seven levels of structural hierarchy. The approaches we develop are directly applicable to other proteinaceous materials.

Secondary fibril structure is a key component of the mechanical properties of protein materials like silk, yet, limited information is known about the internal structure of these protein fibrils. Here, the authors report on the use of polarised Raman and FTIR spectroscopy to study silk materials and identify six distinct secondary structures.

In silico structural and functional characterization of Antheraea mylitta cocoonase

BACKGROUND

Cocoonase is a serine protease present in sericigenous insects and majorly involved in dissolving of sericin protein allowing moth to escape. Cocoon structure is made up of sericin protein which holds fibroin filaments together. Cocoonase enzyme hydrolyzes sericin protein without harming the fibroin. However, until date, no detailed characterization of cocoonase enzyme and its presence in wild silk moth Antheraea mylitta has been carried out. Therefore, current study aimed for detailed characterization of amplified cocoonase enzyme, secondary and tertiary structure prediction, sequence and structural alignment, phylogenetic analysis, and computational validation. Several computational tools such as ProtParam, Iterative Threading Assembly Refinement (I-TASSER), PROCHECK, SAVES v6.0, TM-align, Molecular Evolutionary Genetics Analysis (MEGA) X, and Figtree were employed for characterization of cocoonase protein.

RESULTS

The present study elucidates about the isolation of RNA, cDNA preparation, PCR amplification, and in silico characterization of cocoonase from Antheraea mylitta. Here, total RNA was isolated from head region of A. mylitta, and gene-specific primers were designed using Primer3 followed by PCR-based amplification and sequencing. The newly constructed 377-bp length sequence of cocoonase was subjected to in silico characterization. In silico study of A. mylitta cocoonase showed 26% similarity to A. pernyi strain Qing-6 cocoonase using Blastp and belongs to member of chymotrypsin-like serine protease superfamily. From phylogenetic study, it was found that A. mylitta cocoonase sequence is closely related to A. pernyi cocoonase sequence.

CONCLUSIONS

The present study revealed about the detailed in silico characterization of cocoonase gene and encoded protein obtained from A. mylitta head region. The results obtained infer the presence of cocoonase enzyme in the wild silkworm A. mylitta and can be used for cocoon degumming which will be a valuable and cost-effective strategy in silk industry.

Unexpected high toughness of Samia cynthia ricini silk gut

Silk gut fibers were produced from the silkworm Samia cynthia ricini silk glands by the usual procedure of immersion in a mildly acidic solution and subsequent stretching. The morphology of the silk guts was assessed by scanning electron microscopy, and their microstructure was assessed by infrared spectroscopy and X-ray diffraction. It was found that both naturally spun and Samia silk guts share a common semicrystalline microstructure. The mechanical characterization of the silk guts revealed that these fibers show an elastomeric behavior when tested in water, and exhibit a genuine ground state to which the fiber may revert independently of its previous loading history. In spite of its large cross-sectional area compared with naturally spun silk fibers, Samia silk guts show values of work to fracture up to 160 MJ m^-3, much larger than those of most of their natural counterparts, and establish a new record value for this parameter in silk guts.

Cell Adhesion Behaviors on Spider Silk Fibers, Films, and Nanofibers

Silk-based materials have garnered attention for use as medical supplies due to their mechanical toughness and low cytotoxicity. Silkworm silk has been applied as surgical sutures for decades. In contrast, the utilization of spider silk is limited mainly because of its scarcity. Although the biomimicry of spider silk has been developed using recombinant protein expression systems with the use of genetic engineering, the product often results in lower molecular weight and a lack of the N- or C-terminal regions. The incomplete sequence of the spider silk-like protein prevents the objective evaluation of the native spider silk as a medical application and retards the development of spider silk-inspired materials. Here, we reeled the native spider silk directly from live spiders and investigated the cell adhesion behavior based on three kinds of surface topography of spider silk-based substrates, namely, fibers, films, and non-woven fabrics. The cell adhesion behavior was largely influenced by the surface micro/nanostructure rather than the wettability of the surface. This study will contribute to promote the utilization of spider silk in the medical field as a candidate for promising bio-based fibers in the context of sustainable development goals.

Characterization of the genome and silk-gland transcriptomes of Darwin's bark spider (Caerostris darwini)

Natural silks crafted by spiders comprise some of the most versatile materials known. Artificial silks-based on the sequences of their natural brethren-replicate some desirable biophysical properties and are increasingly utilized in commercial and medical applications today. To characterize the repertoire of protein sequences giving silks their biophysical properties and to determine the set of expressed genes across each unique silk gland contributing to the formation of natural silks, we report here draft genomic and transcriptomic assemblies of Darwin's bark spider, Caerostris darwini, an orb-weaving spider whose dragline is one of the toughest known biomaterials on Earth. We identify at least 31 putative spidroin genes, with expansion of multiple spidroin gene classes relative to the golden orb-weaver, Trichonephila clavipes. We observed substantial sharing of spidroin repetitive sequence motifs between species as well as new motifs unique to C. darwini. Comparative gene expression analyses across six silk gland isolates in females plus a composite isolate of all silk glands in males demonstrated gland and sex-specific expression of spidroins, facilitating putative assignment of novel spidroin genes to classes. Broad expression of spidroins across silk gland types suggests that silks emanating from a given gland represent composite materials to a greater extent than previously appreciated. We hypothesize that the extraordinary toughness of C. darwini major ampullate dragline silk may relate to the unique protein composition of major ampullate spidroins, combined with the relatively high expression of stretchy flagelliform spidroins whose union into a single fiber may be aided by novel motifs and cassettes that act as molecule-binding helices. Our assemblies extend the catalog of sequences and sets of expressed genes that confer the unique biophysical properties observed in natural silks.

Expression of spidroin proteins in the silk glands of golden orb-weaver spiders

The expression of spidroins in the major ampullate, minor ampullate, flagelliform, and tubuliform silk glands of Trichonephila clavipes spiders was analyzed using proteomics analysis techniques. Spidroin peptides were identified and assigned to different gene products based on sequence concurrence when compared with the whole genome of the spider. It was found that only a relatively low proportion of the spidroin genes are expressed as proteins in any of the studied glands. In addition, the expression of spidroin genes in different glands presents a wide range of patterns, with some spidroins being found in a single gland exclusively, while others appear in the content of several glands. The combination of precise genomics, proteomics, microstructural, and mechanical data provides new insights both on the design principles of these materials and how these principles might be translated for the production of high-performance bioinspired artificial fibers.

Complexity of Spider Dragline Silk

The tiny spider makes dragline silk fibers with unbeatable toughness, all under the most innocuous conditions. Scientists have persistently tried to emulate its natural silk spinning process using recombinant proteins with a view toward creating a new wave of smart materials, yet most efforts have fallen short of attaining the native fiber’s excellent mechanical properties. One reason for these shortcomings may be that artificial spider silk systems tend to be overly simplified and may not sufficiently take into account the true complexity of the underlying protein sequences and of the multidimensional aspects of the natural self-assembly process that give rise to the hierarchically structured fibers. Here, we discuss recent findings regarding the material constituents of spider dragline silk, including novel spidroin subtypes, nonspidroin proteins, and possible involvement of post-translational modifications, which together suggest a complexity that transcends the two-component MaSp1/MaSp2 system. We subsequently consider insights into the spidroin domain functions, structures, and overall mechanisms for the rapid transition from disordered soluble protein into a highly organized fiber, including the possibility of viewing spider silk self-assembly through a framework relevant to biomolecular condensates. Finally, we consider the concept of “biomimetics” as it applies to artificial spider silk production with a focus on key practical aspects of design and evaluation that may hopefully inform efforts to more closely reproduce the remarkable structure and function of the native silk fiber using artificial methods.

Hybrid sequencing reveals the full-length Nephila pilipes pyriform spidroin 1 (PySp1)

Araneid spider silk glands can spin seven silk types that have task-specific properties owing to the higher order structure of spider silk proteins. This gives silks superior potential as novel biomaterials. Nephila pilipes, the giant golden orb-weaver, is one of the largest spiders and spins silk with exceptional torsional deformation, toughness, and other properties to support its mass; further investigation relies on a complete amino acid sequence. However, there are no full-length N. pilipes spidroin sequences; in fact, across species, most sequences remain fragmentary because of repetitive region assembly difficulties in short-read sequencing. Here, we develop a hybrid sequencing method that utilizes short-read sequencing to identify seven spidroin terminals in N. pilipes, and long-read sequencing to confirm the full-length pyriform spidroin 1 (PySp1) gene. PySp1 is 11,181 base pairs, with a single exon encoding a 3,726 amino acid protein, the QQ(x)4Qx motif, and lower repeat homogenization, distinct characteristics of genera Nephilinae PySp1. The full-length N. pilipes PySp1 sequences sheds light on spidroin evolution and demonstrates a helpful strategy to find full-length spidroins.

Mantle Transcriptome Provides Insights into Biomineralization and Growth Regulation in the Eastern Oyster (Crassostrea virginica)

Growth of the eastern oyster Crassostrea virginica, a major aquaculture species in the USA, is highly variable and not well understood at molecular levels. As growth of mollusks is confined in shells constructed by the mantle, mantle transcriptomes of large (fast-growing) and small (slow-growing) eastern oysters were sequenced and compared in this study. Transcription was observed for 31,186 genes, among which 104 genes were differentially expressed between the large and small oysters, including 48 upregulated and 56 downregulated in large oysters. Differentially expressed genes (DEGs) included genes from diverse pathways highlighting the complexity of shell formation and growth regulations. Seventeen of the 48 upregulated DEGs were related to shell matrix formation, most of which were upregulated in large oysters, indicating that large oysters are more active in biomineralization and shell formation. Genomic and transcriptomic analyses identified 22 genes encoding novel polyalanine containing proteins (Pacps) with characteristic motifs for matrix function that are tandemly duplicated on one chromosome, all specifically expressed in mantle and at higher levels in large oysters, suggesting that these expanded Pacps play important roles in shell formation and growth. Analysis of sequence variation identified 244,964 SNPs with 328 associated with growth. This study provides novel candidate genes and markers for shell formation and growth, and suggests that genes related to shell formation are important for the complex regulation of growth in the eastern oyster and possibly other bivalve mollusks. Results of this study show that both transcriptional modulation and functional polymorphism are important in determining growth.

Connecting materials, performance and evolution: a case study of the glue of moth-catching spiders (Cyrtarachninae)

Morphological structures and extended phenotypes are made possible by materials that are encoded by the genome. Nearly all biomaterials are viscoelastic, which means that to understand performance, one must understand the strain rate-dependent properties of these materials in relevant ecological interactions, as the behavior of a material can vary dramatically and rapidly. Spider silks are an example of materials whose properties vary substantially intra- and inter-specifically. Here, we focus on aggregate silk, which functions as a biological adhesive. As a case study to understand how a material manifests from genome through organism to ecology, we highlight moth-specialist spiders, the Cyrtarachninae, and their glues as an ideal experimental system to investigate the relationship between genomics and ecologically variable performance of a biological material. There is a clear eco-evolutionary innovation that Cyrtarachne akirai and related species have evolved, a unique trait not found in other spiders, a glue which overcomes the scales of moths. By examining traditional orb-weavers, C. akirai and other subfamily members using biomechanical testing and genomic analysis, we argue that we can track the evolution of this novel bioadhesive and comment on the selection pressures influencing prey specialization. The importance of the ecological context of materials testing is exemplified by the poor performance of C. akirai glue on glass and the exceptional spreading ability and adhesive strength on moths. The genetic basis for these performance properties is experimentally tractable because spider silk genes are minimally pleiotropic and advances in genomic technologies now make possible the discovery of complete silk gene sequences.

Comparative proteomics for an in-depth understanding of bioadhesion mechanisms and evolution across metazoans

Bioadhesion is a critical process for many marine and freshwater invertebrate animals. Bioadhesives mainly made of proteins have remarkable adhesive ability underwater. Unraveling the molecular composition of bioadhesives is fundamental to understanding their physiological roles as well as their potential for biotechnology applications and antibiofouling strategies. With the development of high-throughput methods such as proteomics, bioadhesive protein data in diverse taxa are rapidly accumulating, but the common mechanism across species is elusive due to the vast variety of bioadhesives. In this review, bioadhesive proteins from various taxa are reviewed, with the aim of facilitating researchers to appreciate the diversity of bioadhesive proteins (mostly 20-40) across species. By comparing proteomes across species, it was found that glycine-rich, epidermal growth factor, peroxidase, and DOPA together with typical extracellular domains are the most commonly used domains. Additionally, permanent and temporary adhesion show obvious differences in terms of domains or proteins. A basic recipe for bioadhesives composed of six components is proposed: structural elements, extracellular domains, modification enzymes, proteinase inhibitors, cytoskeletal proteins, and others. The extracellular domains are mostly related to interactions with other macromolecules (proteins, carbohydrates, and lipids), suggesting that domain shuffling and macromolecule interaction might be fundamental for bioadhesive evolution.