A new twist on sea silk: the peculiar protein ultrastructure of fan shell and pearl oyster byssus

Invasive mussels fashion silk-like byssus via mechanical processing of massive horizontally acquired coiled coils

Zebra and quagga mussels (Dreissena spp.) are invasive freshwater biofoulers that perpetrate devastating economic and ecological impact. Their success depends on their ability to anchor onto substrates with protein-based fibers known as byssal threads. Yet, compared to other mussel lineages, little is understood about the proteins comprising their fibers or their evolutionary history. Here, we investigated the hierarchical protein structure of Dreissenid byssal threads and the process by which they are fabricated. Unique among bivalves, we found that threads possess a predominantly β-sheet crystalline structure reminiscent of spider silk. Further analysis revealed unexpectedly that the Dreissenid thread protein precursors are mechanoresponsive α-helical proteins that are mechanically processed into β-crystallites during thread formation. Proteomic analysis of the byssus secretory organ and byssus fibers revealed a family of ultrahigh molecular weight (354 to 467 kDa) asparagine-rich (19 to 20%) protein precursors predicted to form α-helical coiled coils. Moreover, several independent lines of evidence indicate that the ancestral predecessor of these proteins was likely acquired via horizontal gene transfer. This chance evolutionary event that transpired at least 12 Mya has endowed Dreissenids with a distinctive and effective fiber formation mechanism, contributing significantly to their success as invasive species and possibly, inspiring new materials design.

Additives, plasticizers, small microplastics (<100 μm), and other microlitter components in the gastrointestinal tract of commercial teleost fish: Method of extraction, purification, quantification, and characterization using Micro-FTIR

One of the aims of this study is the development of a pretreatment method for additives, plasticizers and other components of micro-litter (APFs), and small microplastics (SMPs <100 μm) in the gastrointestinal tract (GIT) of five of the most widely distributed and consumed commercial fish species, Engraulis encrasiculos, Sardina pilchardus, Mullus surmuletus, Solea solea, and Sparus aurata. The second aim was to develop a simultaneous quantification and identification method via Micro-FTIR of APFs and SMPs ingested by these commercial fish species. The distribution of SMPs and APFs is characteristically different for each species investigated. E. encrasiculos and S. pilchardus had a higher weight of SMPs than the other species investigated. Regarding APFs, the highest abundance was observed in E. encrasiculos. This study highlights the importance of studying additives and plasticizers that can be used as efficient proxies of microplastics, as shown by the presence of vulcanizing agents such as Vanax®.

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.

The byssal-producing glands and proteins of the silverlip pearl oyster Pinctada maxima (Jameson, 1901)

Pinctada maxima are most well known for their production of high-quality natural pearls. They also generate another natural material, the byssus, an adhesive thread critical for steadfast attachment underwater. Herein, P. maxima byssal threads were analysed via proteotranscriptomics to reveal 49 proteins. Further characterisation was undertaken on five highly expressed genes: glycine-rich thread protein (GRT; also known as PUF3), apfp1/perlucin-like protein (Pmfp1); peroxidase; thrombospondin 1, and Balbiani ring 3 (BR3), which showed localised tissue expression. The spatial distribution of GRT and Pmfp1 via immunodetection combined with histology helped to identify glandular regions of the foot that contribute to byssal thread production: the byssal gland, the duct gland, and two thread-forming glands of basophilic and acidophilic serous-like cells. This work advanced primary knowledge on the glands involved in the creation of byssal threads and the protein composition of the byssus for P. maxima, providing a platform for the design of marine biopolymers.

Activation of extracellular electron network in non-electroactive bacteria by Bombyx mori silk

Extracellular electron transfer material (EETM) has increasingly attracted attentions for the enhancing effect on multiple microbial reactions. Especially, EETM is known to be essential to activate the energy network in non-electroactive bacteria. It is motivated to find out an EETM which is natural-based, environmentally friendly, and easily produced at large-scale. In this study, Bombyx mori silk is found, for the first time, to function as an EETM by using an EETM-dependent pentachlorophenol (PCP) dechlorinating anaerobic microbial culture. Subsequently, by dividing fibroin fiber into different soluble/insoluble fractions and correlating their EET functions with their structural properties based on various spectroscopic analyses, the β-sheet configuration is suggested as an essential structure supporting the EET function of silk materials. The analyses also suggested the involvement of sulfur-containing amino acids in this function. The EET function is not degraded by boiling or acid/alkaline treatments and the material can be utilized multiple times, although it is susceptible to UV irradiation. Bombyx mori silk also enhance other microbial reactions, including Fe(III)OOH reduction, CO₂ reduction to acetate, and nitrogen fixation. This discovery provides a basis for developing biotechnology for environmental remediation, global warming reduction, and biofertilizer production using Bombyx mori silk and its wastes.

Diverse silk and silk-like proteins derived from terrestrial and marine organisms and their applications

Organisms develop unique systems in a given environment. In the process of adaptation, they employ materials in a clever way, which has inspired mankind extensively. Understanding the behavior and material properties of living organisms provides a way to emulate these natural systems and engineer various materials. Silk is a material that has been with human for over 5000 years, and the success of mass production of silkworm silk has realized its applications to medical, pharmaceutical, optical, and even electronic fields. Spider silk, which was characterized later, has expanded the application sectors to textile and military materials based on its tough mechanical properties. Because silk proteins are main components of these materials and there are abundant creatures producing silks that have not been studied, the introduction of new silk proteins would be a breakthrough of engineering materials to open innovative industry fields. Therefore, in this review, we present diverse silk and silk-like proteins and how they are utilized with respect to organism's survival. Here, the range of organisms are not constrained to silkworms and spiders but expanded to other insects, and even marine creatures which produce silk-like proteins that are not observed in terrestrial silks. This viewpoint broadening of silk and silk-like proteins would suggest diverse targets of engineering to design promising silk-based materials. STATEMENT OF SIGNIFICANCE: Silk has been developed as a biomedical material due to unique mechanical and chemical properties. For decades, silks from various silkworm and spider species have been intensively studied. More recently, other silk and silk-like proteins with different sequences and structures have been reported, not only limited to terrestrial organisms (honeybee, green lacewing, caddisfly, and ant), but also from marine creatures (mussel, squid, sea anemone, and pearl oyster). Nevertheless, there has hardly been well-organized literature on silks from such organisms. Regarding the relationship among sequence-structure-properties, this review addresses how silks have been utilized with respect to organism's survival. Finally, this information aims to improve the understanding of diverse silk and silk-like proteins which can offer a significant interest to engineering fields.

Following the thread: Mytilus mussel byssus as an inspired multi-functional biomaterial

Over the last 15 years, the byssus of marine mussels (Mytilus spp.) has emerged as an important model system for the bio-inspired development and synthesis of advanced polymers and adhesives. But how did these seemingly inconsequential fibers that are routinely discarded in mussel hors d’oeuvres become the focus of intense international research. In the present review, we take a historical perspective to understand this phenomenon. Our purpose is not to review the sizeable literature of mussel-inspired materials, as there are numerous excellent reviews that cover this topic in great depth. Instead, we explore how the byssus became a magnet for bio-inspired materials science, with a focus on the specific breakthroughs in the understanding of composition, structure, function, and formation of the byssus achieved through fundamental scientific investigation. Extracted principles have led to bio-inspired design of novel materials with both biomedical and technical applications, including surgical adhesives, self-healing polymers, tunable hydrogels, and even actuated composites. Continued study into the byssus of Mytilid mussels and other species will provide a rich source of inspiration for years to come.

A non-lethal method to assess element content in the endangered Pinna nobilis

The fan shell Pinna nobilis is the largest bivalve endemic to the Mediterranean and is actually a strongly endangered species. Due to the biological, ecological, and historical relevance of this species, the research of a non-lethal method to relate the element content in organism's tissues and environment can provide information potentially useful to evaluate environmental pollution and organism physiological status. In this study, a screening on element concentration in the animal growing environment (seawater and sediments) and in four soft tissues (hepatopancreas, gills, mantle, and muscle), and two acellular tissues (calcite shell layer, and byssus) was performed. The comparison among these results was used to assess whether the no-lethal acellular tissue element concentration can be used to reveal the element presence in the environment and soft tissues. Elements, such as B, Ag, As, Mn, Mo, Pb, or Se, showed a possible relationship between their presence in the byssus and soft tissues. In the byssus Cr, Sb, Sn, and V have shown to be mostly related to the environment, more than the soft tissues, and might be used to draw a historical record of the exposure of the organism. The element concentration in the calcite shell layer did not relate with environmental element concentrations. Essential elements, like Cu, Fe, Ni, and Zn, were present in calcite shell layer and byssus and are likely related to their biological activity in the organism. The research also gave an overview on the presence of pollution and on the preferential intake route of the element. In summary, this study, performed on a limited number of specimens of this protected species, indicated that element concentration in the byssus can be applied as non-lethal method to monitor this endangered species and its interaction with the elements in the growing environment.

Structure, function and parallel evolution of the bivalve byssus, with insights from proteomes and the zebra mussel genome

The byssus is a structure unique to bivalves. Byssal threads composed of many proteins extend like tendons from muscle cells, ending in adhesive pads that attach underwater. Crucial to settlement and metamorphosis, larvae of virtually all species are byssate. By contrast, in adults, the byssus is scattered throughout bivalves, where it has had profound effects on morphological evolution and been key to adaptive radiations of epifaunal species. I compare byssus structure and proteins in blue mussels (Mytilus), by far the best characterized, to zebra mussels (Dreissena polymorpha), in which several byssal proteins have been isolated and sequenced. By mapping the adult byssus onto a recent phylogenomic tree, I confirm its independent evolution in these and other lineages, likely parallelisms with common origins in development. While the byssus is superficially similar in Dreissena and Mytilus, in finer detail it is not, and byssal proteins are dramatically different. I used the chromosome-scale D. polymorpha genome we recently assembled to search for byssal genes and found 37 byssal loci on 10 of the 16 chromosomes. Most byssal genes are in small families, with several amino acid substitutions between paralogs. Byssal proteins of zebra mussels and related quagga mussels (D. rostriformis) are divergent, suggesting rapid evolution typical of proteins with repetitive low complexity domains. Opportunities abound for proteomic and genomic work to further our understanding of this textbook example of a marine natural material. A priority should be invasive bivalves, given the role of byssal attachment in the spread of, and ecological and economic damage caused by zebra mussels, quagga mussels and others. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.

Identification of novel adhesive proteins in pearl oyster by proteomic and bioinformatic analysis

Byssuses, which are proteinaceous fibers secreted by mollusks, are remarkable underwater adhesives. Although mussel adhesives are well known, much less is known about the byssal proteins of pearl oysters especially in the adhesive regions. In this study, adhesive proteins from the pearl oyster Pinctada fucata were studied in depth by transcriptomics and proteomics approaches. In total, 16 novel proteins were identified including a von Willebrand factor type A domain-containing protein, a thrombospondin-1-like protein, tyrosinase, mucin-like proteins, protease inhibitors, and Pinctada unannotated foot protein 3 (PUF3) to PUF6. Interestingly, PUF3-6 are enriched with glycine, serine, and PXG (X = F/Y/W/K/L) motifs and are highly expressed in the foot. The identification of byssal proteins of the pearl oyster is a key step for understanding byssus formation and may inspire the synthesis of novel adhesives for underwater use and the development of anti-biofouling strategies.

Evidence of small microplastics (<100 μm) ingestion by Pacific oysters (Crassostrea gigas): A novel method of extraction, purification, and analysis using Micro-FTIR

Microplastics (MPs) are present in fresh, brackish, or marine waters. Micro- and macroinvertebrates can mistake MPs or small microplastics (SMPs, <100 μm) to be food particles and easily ingest them according to the size of their mouthparts. SMPs may then block the passage of food through the intestinal tract (i.e. hepatopancreas), accumulate within the organism, and enter the food web. Pacific oysters (Crassostrea gigas) are allochthonous filter-feeding bivalve mollusks, which have been introduced in coastal seas around the world in both natural banks and farms. Considering their economic and ecological value, these bivalves have been chosen as a model to study the ingestion of SMPs. A novel method for the extraction and purification of SMPs in bivalves was developed. Quantification and simultaneous polymer identification of SMPs using Micro-FTIR (Fourier Transform Infrared Spectroscopy) were performed, with a limit of detection for the particle size of 5 μm.

A sugar-lectin rich interface between soft tissue and the stiff byssus of Atrina pectinata

Maintaining durable adhesion between soft tissues and relatively hard implant materials is one of the most elusive technological difficulties in bionic devices due to contact damage between mechanically mismatched materials. Although there are many examples of coexistence of soft and hard tissues in living organisms, relatively little is known about the mechanisms used to overcome mechanical mismatches occurring at the interface between soft and hard tissues. Among the various creatures possessing mechanically mismatched biological tissues, Atrina pectinata is a good model system where the interface between stiff byssal threads and soft tissues is distributed all over an extended organ. In this study, we found a wide distribution of various types of carbohydrates and lectins at the mechanically mismatched interface of the byssus of Atrina using histological methods and proteomics. Reversible and robust interactions between the carbohydrate and lectins at the interface would play a major role in mitigating the contact damage at the Atrina interface. Based on these results, the adhesion between sugar and lectin would be useful to overcome a wide range of contact damage observed in research studies on bionic devices.

Self-healing silk from the sea: role of helical hierarchical structure in Pinna nobilis byssus mechanics

The byssus fibers of Mytilus mussel species have become an important role model in bioinspired materials research due to their impressive properties (e.g. high toughness, self-healing); however, Mytilids represent only a small subset of all byssus-producing bivalves. Recent studies have revealed that byssus from other species possess completely different protein composition and hierarchical structure. In this regard, Pinna nobilis byssus is especially interesting due to its very different morphology, function and its historical use for weaving lightweight golden fabrics, known as sea silk. P. nobilis byssus was recently discovered to be comprised of globular proteins organized into a helical protein superstructure. In this work, we investigate the relationships between this hierarchical structure and the mechanical properties of P. nobilis byssus threads, including energy dissipation and self-healing capacity. To achieve this, we performed in-depth mechanical characterization, as well as tensile testing coupled with in situ X-ray scattering. Our findings reveal that P. nobilis byssus, like Mytilus, possesses self-healing and energy damping behavior and that the initial elastic behavior of P. nobilis byssus is due to stretching and unraveling of the previously observed helical building blocks comprising the byssus. These findings have biological relevance for understanding the convergent evolution of mussel byssus for different species, and also for the field of bio-inspired materials.

Fibers on the Fly: Multiscale Mechanisms of Fiber Formation in the Capture Slime of Velvet Worms

Many organisms have evolved a capacity to form biopolymeric fibers outside their bodies for functions such as defense, prey capture, attachment, and protection. In particular, the adhesive capture slime of onychophorans (velvet worms) is remarkable for its ability to rapidly form stiff fibers through mechanical drawing. Notably, fibers that are formed ex vivo from extracted slime can be dissolved in water and new fibers can be drawn from the solution, indicating that fiber formation is encoded in the biomolecules that comprise the slime. This review highlights recent findings on the biochemical and physicochemical principles guiding this circular process in the Australian onychophoran Euperipatoides rowelli. A multiscale cross-disciplinary approach utilizing techniques from biology, biochemistry, physical chemistry, and materials science has revealed that the slime is a concentrated emulsion of nanodroplets comprised primarily of proteins, stabilized via electrostatic interactions, possibly in a coacervate phase. Upon mechanical agitation, droplets coalesce, leading to spontaneous self-assembly and fibrillation of proteins—a completely reversible process. Recent investigations highlight the importance of subtle transitions in protein structure and charge balance. These findings have clear relevance for better understanding this adaptive prey capture behavior and providing inspiration toward sustainable polymer processing.

In Silico Analysis of Pacific Oyster (Crassostrea gigas) Transcriptome over Developmental Stages Reveals Candidate Genes for Larval Settlement

Following their planktonic phase, the larvae of benthic marine organisms must locate a suitable habitat to settle and metamorphose. For oysters, larval adhesion occurs at the pediveliger stage with the secretion of a proteinaceous bioadhesive produced by the foot, a specialized and ephemeral organ. Oyster bioadhesive is highly resistant to proteomic extraction and is only produced in very low quantities, which explains why it has been very little examined in larvae to date. In silico analysis of nucleic acid databases could help to identify genes of interest implicated in settlement. In this work, the publicly available transcriptome of Pacific oyster Crassostrea gigas over its developmental stages was mined to select genes highly expressed at the pediveliger stage. Our analysis revealed 59 sequences potentially implicated in adhesion of C. gigas larvae. Some related proteins contain conserved domains already described in other bioadhesives. We propose a hypothetic composition of C. gigas bioadhesive in which the protein constituent is probably composed of collagen and the von Willebrand Factor domain could play a role in adhesive cohesion. Genes coding for enzymes implicated in DOPA chemistry were also detected, indicating that this modification is also potentially present in the adhesive of pediveliger larvae.