Biomacromolecules within bivalve shells: Is chitin abundant?

Assessing marine ecosystem health using multi-omic analysis of blue mussel liquid biopsies: A case study within a national marine park

Marine ecosystems are under escalating threats from myriad environmental stressors, necessitating a deeper understanding of their impact on biodiversity and the health of sentinel organisms. In this study, we carried out a spatiotemporal multi-omic analysis of liquid biopsies collected from mussels (Mytilus spp.) in marine ecosystems of a national park. We delved into the epigenomic, transcriptomic, glycomic, proteomic, and microbiomic profiles to unravel the intricate interplay between ecosystem biodiversity and mussels' biological response to their environments. Our analysis revealed temporal fluctuations in the alpha diversity of the circulating microbiome associated with human activities. Analysis of the hemolymphatic circulating cell-free DNA (ccfDNA) provided information on the biodiversity and the presence of potential pathogens. Epigenomic analysis revealed widespread hypomethylation sites within the mitochondrial (mtDNA). Comparative transcriptomic and glycomic analyses highlighted differences in metabolic pathways and genes associated with immune and wound healing functions. This study demonstrates the potential of multi-omic analysis of liquid biopsy in sentinel to provide a holistic view of human activities' environmental impacts on marine coastal ecosystems. Overall, this approach has the potential to enhance the effectiveness and efficiency of various conservation efforts, leading to more informed decision-making and better outcomes for biodiversity and ecosystem conservation.

Structure and function of the periostracum in the bivalve Perna viridis

The periostracum is an outermost coating of all shelled-molluscs such as bivalves, corresponding to the interfacial layer separating the calcareous shells from the environment. It therefore plays a key role in the growth and survival of bivalves. Nevertheless, the periostracum has attracted little attention. Here, using the optical microscope (OM) and field-emission scanning electron microscope (FE-SEM), we investigate the structure and variation of the periostracum in the green mussel Perna viridis. We find that this periostracum has a novel sandwich structure with an outer (ODL) and inner dense layer (IDL) interleaved with a middle fibrous layer (MFL). The latter consists of locally parallel fibers (57-112 nm wide) and exhibits rich iridescent colors with a reversible hydrochromic behavior. Moreover, we find that this periostracum shows a significant variation in individual shells. Impressively, its thickness varies continuously along the shell edge. In addition, the periostracum at the ventral region is not only the thickest in a shell but also reinforced with the inorganic phosphate. We assume that this unusual variation in a same shell probably originates form defensive adaptations to predation and abrasion. Although many questions remain unanswered, this work reveals a new structure model of the periostracum, which not only advances our understanding of the periostracal formation mechanism, but also provides a natural prototype for design and synthesis of biomimetic coating and photonic materials.

Material and Environmental Properties of Natural Polymers and Their Composites for Packaging Applications—A Review

The current trend of using plastic material in the manufacturing of packaging products raises serious environmental concerns due to waste disposal on land and in oceans and other environmental pollution. Natural polymers such as cellulose, starch, chitosan, and protein extracted from renewable resources are extensively explored as alternatives to plastics due to their biodegradability, biocompatibility, nontoxic properties, and abundant availability. The tensile and water vapor barrier properties and the environmental impacts of natural polymers played key roles in determining the eligibility of these materials for packaging applications. The brittle behavior and hydrophilic nature of natural polymers reduced the tensile and water vapor barrier properties. However, the addition of plasticizer, crosslinker, and reinforcement agents substantially improved the mechanical and water vapor resistance properties. The dispersion abilities and strong interfacial adhesion of nanocellulose with natural polymers improved the tensile strength and water vapor barrier properties of natural polymer-based packaging films. The maximum tensile stress of these composite films was about 38 to 200% more than that of films without reinforcement. The water vapor barrier properties of composite films also reduced up to 60% with nanocellulose reinforcement. The strong hydrogen bonding between natural polymer and nanocellulose reduced the polymer chain movement and decreased the percent elongation at break up to 100%. This review aims to present an overview of the mechanical and water vapor barrier properties of natural polymers and their composites along with the life cycle environmental impacts to elucidate their potential for packaging applications.

The proteomics of the freshwater pearl powder: Insights from biomineralization to biomedical application

The freshwater pearl is one kind of valuable organic jewelry and traditional Chinese medicine (TCM). However, the molecular basis of matrix protein in pearl biomineralization and biomedical applications are largely unknown to date. In this study, the matrix proteins of water-soluble matrix, acid-soluble matrix and acid-insoluble matrix from the freshwater seedless pearl powder were detected using liquid chromatography-tandem mass spectrometry (LC-MS/MS) respectively, and identified against the transcriptomic database of the pearl sac. The results showed that a total of 190 proteins were identified in pearl proteomics, which was divided into eight categories by their potential biomineralization functions. The composition of pearl matrix proteins and the high frequency conserved domains like carbonic anhydrase, von Willebrand factor type A, tyrosinase and chitin binding 2 in protein sequences, implying that the "chitin-silk fibroin gel proteins-acidic macromolecules" model was suitable for description the pearl biomineralization process. Meanwhile, ninety-one of pearl matrix proteins could be classified into seven categories by their potential medical functions including wound healing, osteogenic property, antioxidant activity, neuro-regulation effects, skin lightening effect, anti-inflammatory and anti-apoptotic effects and other immunomodulatory property. In general, these results provided valuable new insights into not only the diversity of pearl matrix protein for mollusc biomineralization, but the molecular basis of pearl matrix proteins responsible for their diverse biological properties in TCM application. SIGNIFICANCE: The significance of this study included the following points.

Identification and Phylogenetic Analysis of Chitin Synthase Genes from the Deep-Sea Polychaete Branchipolynoe onnuriensis Genome

Chitin, one of the most abundant biopolymers in nature, is a crucial material that provides sufficient rigidity to the exoskeleton. In addition, chitin is a valuable substance in both the medical and industrial fields. The synthesis of chitin is catalyzed by chitin synthase (CHS) enzymes. Although the chitin synthesis pathway is highly conserved from fungi to invertebrates, CHSs have mostly only been investigated in insects and crustaceans. Especially, little is known about annelids from hydrothermal vents. To understand chitin synthesis from the evolutionary view in a deep-sea environment, we first generated the whole-genome sequencing of the parasitic polychaete Branchipolynoe onnuriensis. We identified seven putative CHS genes (BonCHS1-BonCHS7) by domain searches and phylogenetic analyses. This study showed that most crustaceans have only a single copy or two gene copies, whereas at least two independent gene duplication events occur in B. onnuriensis. This is the first study of CHS obtained from a parasitic species inhabiting a hydrothermal vent and will provide insight into various organisms’ adaptation to the deep-sea hosts.

Pressure-induced crystallization and densification of amorphized calcium carbonate hexahydrate controlled by interfacial water

Amorphous calcium carbonate (ACC) is widely known as a metastable precursor in the formation of crystalline calcium carbonate biominerals. However, the exact role of water during the crystallization of ACC remains elusive. Here, a novel ACC with high specific surface area and nanopores is synthesized by solvent-induced dehydration and amorphization of crystalline calcium carbonate hexahydrate (ikaite), denoted as I-ACC. Comparing I-ACC and typical spherical ACC (S-ACC) nanoparticles, it reveals that the crystallization pathways of ACC under heating or pressure are not dictated by the total amount of water in ACC as reported, but rather the interfacial water that is released from ACC bulk and adsorbed on the surface of the particles. We show that the crystallization pathways of I-ACC to calcite single crystal with high specific surface area or vaterite can be easily controlled by tuning the release of water during heating. In addition, densely packed pure vaterite can be obtained via pressured-induced transformation of I-ACC at room temperature, which is otherwise difficult to form using S-ACC. These insights contribute to the understanding of the biological control of mineral formation via amorphous precursors and offer new opportunities to bioprocess inspired fabrication of strong bulk material at room temperature.

Organic biopolymers of venus clams: Collagen-related matrix in the bivalve shells with crossed-lamellar ultrastructure

BACKGROUND

Biochemical studies and spectroscopic techniques have shown that chitin-silk fibroins are common in nacroprismatic bivalve shells. However, the nature of organic biopolymers in the less well studied shell architectures, such as crossed lamellar shells, remain unknown. Here, two venus shells, Callista disrupta and Callista kingii, with crossed lamellar ultrastructure have been studied.

METHODS

We employed thermal gravimetric analysis, optical-, confocal- and scanning electron-microscopes, gel-sodium dodecyl sulfate (gel-SDS), FTIR, ultra-performance liquid chromatography and high-performance anion-exchange chromatography system with pulsed amperometric detection to analyse organic macromolecules in the shells.

RESULTS

Thermal analysis showed a low concentration of organic macromolecules in C. disrupta (1.38 wt%) and in C. kingii (1.71 wt%). A combination of biochemical protocols, including Calcofluor White staining and FTIR spectroscopic assessment, indicate that amino-polysaccharide chitin together with proteins, are present in the organic scaffolding of the shells. Scanning electron microscope of insoluble acid biopolymer extracts as well as FTIR technique show that the hierarchical structural organizations of organic biopolymers consist collagen-related matrix. Our histochemical fixing and staining techniques reveal many discrete proteins and glycoproteins from soluble organic macromolecules on the gel-SDS. We show here 'singlet' and 'doublet' glycosaminoglycan bands that are far above 260 kDa.

GENERAL SIGNIFICANCE/CONCLUSIONS

The presence of collagen matrix in Callista shells shows promise for the new source of biomaterials. Most importantly, the structural organization of the proteinaceous motif is predominantly helical structures and not silk-fibroin unlike in nacreous bivalve shells.

The 'Shellome' of the Crocus Clam Tridacna crocea Emphasizes Essential Components of Mollusk Shell Biomineralization

Molluscan shells are among the most fascinating research objects because of their diverse morphologies and textures. The formation of these delicate biomineralized structures is a matrix-mediated process. A question that arises is what are the essential components required to build these exoskeletons. In order to understand the molecular mechanisms of molluscan shell formation, it is crucial to identify organic macromolecules in different shells from diverse taxa. In the case of bivalves, however, taxon sampling in previous shell proteomics studies are focused predominantly on representatives of the class Pteriomorphia such as pearl oysters, edible oysters and mussels. In this study, we have characterized the shell organic matrix from the crocus clam, Tridacna crocea, (Heterodonta) using various biochemical techniques, including SDS-PAGE, FT-IR, monosaccharide analysis, and enzyme-linked lectin assay (ELLA). Furthermore, we have identified a number of shell matrix proteins (SMPs) using a comprehensive proteomics approach combined to RNA-seq. The biochemical studies confirmed the presence of proteins, polysaccharides, and sulfates in the T. crocea shell organic matrix. Proteomics analysis revealed that the majority of the T. crocea SMPs are novel and dissimilar to known SMPs identified from the other bivalve species. Meanwhile, the SMP repertoire of the crocus clam also includes proteins with conserved functional domains such as chitin-binding domain, VWA domain, and protease inhibitor domain. We also identified BMSP (Blue Mussel Shell Protein, originally reported from Mytilus), which is widely distributed among molluscan shell matrix proteins. Tridacna SMPs also include low-complexity regions (LCRs) that are absent in the other molluscan genomes, indicating that these genes may have evolved in specific lineage. These results highlight the diversity of the organic molecules – in particular proteins – that are essential for molluscan shell formation.

Diversified Biomineralization Roles of Pteria penguin Pearl Shell Lectins as Matrix Proteins

Previously, we isolated jacalin-related lectins termed PPL2, PPL3 (PPL3A, 3B and 3C) and PPL4 from the mantle secretory fluid of Pteria penguin (Mabe) pearl shell. They showed the sequence homology with the plant lectin family, jacalin-related β-prism fold lectins (JRLs). While PPL3s and PPL4 shared only 35%–50% homology to PPL2A, respectively, they exhibited unique carbohydrate binding properties based on the multiple glycan-binding profiling data sets from frontal affinity chromatography analysis. In this paper, we investigated biomineralization properties of these lectins and compared their biomineral functions. It was found that these lectins showed different effects on CaCO₃ crystalization, respectively, although PPL3 and PPL2A showed similar carbohydrate binding specificities. PPL3 suppressed the crystal growth of CaCO₃ calcite, while PPL2A increased the number of contact polycrystalline calcite composed of more than one crystal with various orientations. Furthermore, PPL4 alone showed no effect on CaCO₃ crystalization; however, PPL4 regulated the size of crystals collaborated with N-acetyl-D-glucosamine and chitin oligomer, which are specific in recognizing carbohydrates for PPL4. These observations highlight the unique functions and molecular evolution of this lectin family involved in the mollusk shell formation.

Influence of proteins on mechanical properties of a natural chitin-protein composite

In many biogenic materials, chitin chains are assembled in fibrils that are wrapped by a protein fold. In them, the mechanical properties are supposed to be related to intra- and inter- interactions among chitin and proteins. This hypothesis has been poorly investigated. Here, this research theme is studied using the pen of Loligo vulgaris as a model material of chitin-protein composites. Chemical treatments were used to change the interactions involving only the proteic phase, through unfolding and/or degradation processes. Successively, structural and mechanical parameters were examined using spectroscopy, microscopy, X-ray diffractometry, and tensile tests. The data analysis showed that chemical treatments did not modify the structure of the chitin matrix. This allowed to derive from the mechanical test analysis the following conclusions: (i) the maximum stress (σ_max) relies on the presence of the disulfide bonds; (ii) the Young's modulus (E) relies on the overall correct folding of the proteins; (iii) the whole removal of proteins induces a decrease of E (> 90%) and σ_max (> 80%), and an increase in the maximum elongation. These observations indicate that in the chitin matrix the proteins act as a strengthener, which efficacy is controlled by the presence of disulfide bridges. This reinforcement links the chitin fibrils avoiding them to slide one on the other and maximizing their resistance and stiffness. In conclusion, this knowledge can explain the physio-chemical properties of other biogenic polymeric composites and inspire the design of new materials. STATEMENT OF SIGNIFICANCE: To date, no study has addressed on how proteins influence chitin-composite material's mechanical properties. Here we show that the Young's modulus and the maximum stress mainly rely on protein disulfide bonds, the inter-proteins ones and those controlling the folding of chitin-binding domains. The removal of protein matrix induce a reduction of Young's modulus and maximum stress, leaving the chitin matrix structurally unaltered. The measure of the maximum elongation shows that the chitin fibrils slide on each other only after removing the protein matrix. In conclusion, this research shows that the proteins act as a stiff matrix reinforced by di-sulfide bridges that link crystalline chitin fibrils avoiding them to slide one on the other.

Characterization of organophosphatic brachiopod shells: spectroscopic assessment of collagen matrix and biomineral components

The shells of linguloid brachiopods such as Lingula and Discinisca are inorganic-organic nanocomposites with a mineral phase of calcium phosphate (Ca-phosphate). Collagen, the main extracellular matrix in Ca-phosphatic vertebrate skeletons, has not previously been clearly resolved at the molecular level in organophosphatic brachiopods. Here, modern and recently-alive linguliform brachiopod shells of Lingula and Discinisca have been studied by microRaman spectroscopy, Fourier transform infrared spectroscopy, field emission gun scanning electron microscopy, and thermal gravimetric analysis. For the first time, biomineralized collagen matrix and Ca-phosphate components were simultaneously identified, showing that the collagen matrix is an important moiety in organophosphatic brachiopod shells, in addition to prevalent chitin. Stabilized nanosized apatitic biominerals (up to ∼50 nm) permeate the framework of organic fibrils. There is a ∼2.5-fold higher wt% of carbonate (CO₃ ^2-) in Lingula versus Discinisca shells. Both microRaman spectroscopy and infrared spectra show transient amorphous Ca-phosphate and octacalcium phosphate components. For the first time, trivalent moieties at ∼1660 cm^-1 and divalent moieties at ∼1690 cm^-1 in the amide I spectral region were identified. These are related to collagen cross-links that are abundant in mineralized tissues, and could be important features in the biostructural and mechanical properties of Ca-phosphate shell biominerals. This work provides a critical new understanding of organophosphatic brachiopod shells, which are some of the earliest examples of biomineralization in still-living animals that appeared in the Cambrian radiation.

A Nature’s Curiosity: The Argonaut “Shell” and Its Organic Content

Molluscs are known for their ability to produce a calcified shell resulting from a genetically controlled and matrix-mediated process, performed extracellularly. The occluded organic matrix consists of a complex mixture of proteins, glycoproteins and polysaccharides that are in most cases secreted by the mantle epithelium. To our knowledge, the model studied here—the argonaut, also called paper nautilus—represents the single mollusc example where this general scheme is not valid: the shell of this cephalopod is indeed formed by its first dorsal arms pair and it functions as an eggcase, secreted by females only; furthermore, this coiled structure is fully calcitic and the organization of its layered microstructures is unique. Thus, the argonautid shell appears as an apomorphy of this restricted family, not homologous to other cephalopod shells. In the present study, we investigated the physical and biochemical properties of the shell of Argonauta hians, the winged argonaut. We show that the shell matrix contains unusual proportions of soluble and insoluble components, and that it is mostly proteinaceous, with a low proportion of sugars that appear to be mostly sulfated glycosaminoglycans. Proteomics performed on different shell fractions generated several peptide sequences and identified a number of protein hits, not shared with other molluscan shell matrices. This may suggest the recruitment of unique molecular tools for mineralizing the argonaut’s shell, a finding that has some implications on the evolution of cephalopod shell matrices.

Mollusc shellomes: Past, present and future

In molluscs, the shell fabrication requires a large array of secreted macromolecules including proteins and polysaccharides. Some of them are occluded in the shell during mineralization process and constitute the shell repertoire. The protein moieties, also called shell proteomes or, more simply, 'shellomes', are nowadays analyzed via high-throughput approaches. These latter, applied so far on about thirty genera, have evidenced the huge diversity of shellomes from model to model. They also pinpoint the recurrent presence of functional domains of diverse natures. Shell proteins are not only involved in guiding the mineral deposition, but also in enzymatic and immunity-related functions, in signaling or in coping with many extracellular molecules such as saccharides. Many shell proteins exhibit low complexity domains, the function of which remains unclear. Shellomes appear as self-organizing systems that must be approached from the point of view of complex systems biology: at supramolecular level, they generate emergent properties, i.e., microstructures that cannot be simply explained by the sum of their parts. A conceptual scheme is developed here that reconciles the plasticity of the shellome, its evolvability and the constrained frame of microstructures. Other perspectives arising from the study of shellomes are briefly discussed, including the macroevolution of shell repertoires, their maturation and their transformation through time.

An insight into the structure, composition and hardness of a biological material: the shell of freshwater mussels

The shell of the freshwater mussel (Mollusca: Bivalvia) is a composite biological material linked with multifunctional roles in sustaining ecosystem services. Apart from providing mechanical strength and support, the shell is an important site for adherence and growth of multiple types of algae and periphyton. Variations in the shell architecture are observed in the mussels both within a species and among different species. Considering the prospective utility of the shell of the freshwater mussels as a biological material, an assessment of the shell characteristics was accomplished using Corbicula bensoni and Lamellidens marginalis as model species. The calcium carbonate (CaCO₃) content of the shells, physical features and mechanical strength were assessed along with the morphometric analysis. The CaCO₃ content of the shell (upto 95% to 96% of the shell weight) of both the mussels was positively correlated with the shell length, suggesting increased deposition of CaCO₃ in shells with the growth of the species. The cross sectioned views of FE-SEM images of the shells exhibited distinct layered structure with external periostracum and inner nacreous layer varying distinctly. In the growing region, the growth line was prominent in the mussel shells revealed through the FESEM images. In addition XRD, FTIR and EDS studies on the mussel shells confirmed the existence of both aragonite and calcite forms of the calcium carbonate crystals with the incidence of various functional groups. The mechanical strength of the mussel shells was explored through nanoindentation experiments, revealed significant strength at the nanoparticle level of the shells. It was apparent from the results that the shell of the freshwater mussel L. marginalis and C. bensoni qualify as a biological material with prospective multiple applications for human well-being and sustaining environmental quality.

Freshwater mussel shells: prospects as multifunctional biological material.

Structural description of surfaces and interfaces in biominerals by DNP SENS

Biological mineralized tissues are hybrid materials with complex hierarchical architecture composed of biominerals often embedded in an organic matrix. The atomic-scale comprehension of surfaces and organo-mineral interfaces of these biominerals is of paramount importance to understand the ultrastructure, the formation mechanisms as well as the biological functions of the related biomineralized tissue. In this communication we demonstrate the capability of DNP SENS to reveal the fine atomic structure of biominerals, and more specifically their surfaces and interfaces. For this purpose, we studied two key examples belonging to the most significant biominerals family in nature: apatite in bone and aragonite in nacreous shell. As a result, we demonstrate that DNP SENS is a powerful approach for the study of intact biomineralized tissues. Signal enhancement factors are found to be up to 40 and 100, for the organic and the inorganic fractions, respectively, as soon as impregnation time with the radical solution is long enough (between 12 and 24 h) to allow an efficient radical penetration into the calcified tissues. Moreover, ions located at the biomineral surface are readily detected and identified through ³¹P or ¹³C HETCOR DNP SENS experiments. Noticeably, we show that protonated anions are preponderant at the biomineral surfaces in the form of HPO₄^2- for bone apatite and HCO₃^2- for nacreous aragonite. Finally, we demonstrate that organo-mineral interactions can be probed at the atomic level with high sensitivity. In particular, reliable ¹³C-{³¹P} REDOR experiments are achieved in a few hours, leading to the determination of distances, molar proportion and binding mode of citrate bonded to bone mineral in native compact bone. According to our results, only 80% of the total amount of citrate in bone is directly interacting with bone apatite through two out of three carboxylic groups.

Bioinspired Materials: From Living Systems to New Concepts in Materials Chemistry

Nature successfully employs inorganic solid-state materials (i.e., biominerals) and hierarchical composites as sensing elements, weapons, tools, and shelters. Optimized over hundreds of millions of years under evolutionary pressure, these materials are exceptionally well adapted to the specifications of the functions that they perform. As such, they serve today as an extensive library of engineering solutions. Key to their design is the interplay between components across length scales. This hierarchical design—a hallmark of biogenic materials—creates emergent functionality not present in the individual constituents and, moreover, confers a distinctly increased functional density, i.e., less material is needed to provide the same performance. The latter aspect is of special importance today, as climate change drives the need for the sustainable and energy-efficient production of materials. Made from mundane materials, these bioceramics act as blueprints for new concepts in the synthesis and morphosynthesis of multifunctional hierarchical materials under mild conditions. In this review, which also may serve as an introductory guide for those entering this field, we demonstrate how the pursuit of studying biomineralization transforms and enlarges our view on solid-state material design and synthesis, and how bioinspiration may allow us to overcome both conceptual and technical boundaries.

Express Method for Isolation of Ready-to-Use 3D Chitin Scaffolds from Aplysina archeri (Aplysineidae: Verongiida) Demosponge

Sponges are a valuable source of natural compounds and biomaterials for many biotechnological applications. Marine sponges belonging to the order Verongiida are known to contain both chitin and biologically active bromotyrosines. Aplysina archeri (Aplysineidae: Verongiida) is well known to contain bromotyrosines with relevant bioactivity against human and animal diseases. The aim of this study was to develop an express method for the production of naturally prefabricated 3D chitin and bromotyrosine-containing extracts simultaneously. This new method is based on microwave irradiation (MWI) together with stepwise treatment using 1% sodium hydroxide, 20% acetic acid, and 30% hydrogen peroxide. This approach, which takes up to 1 h, made it possible to isolate chitin from the tube-like skeleton of A. archeri and to demonstrate the presence of this biopolymer in this sponge for the first time. Additionally, this procedure does not deacetylate chitin to chitosan and enables the recovery of ready-to-use 3D chitin scaffolds without destruction of the unique tube-like fibrous interconnected structure of the isolated biomaterial. Furthermore, these mechanically stressed fibers still have the capacity for saturation with water, methylene blue dye, crude oil, and blood, which is necessary for the application of such renewable 3D chitinous centimeter-sized scaffolds in diverse technological and biomedical fields.