Soluble silk-like organic matrix in the nacreous layer of the bivalve Pinctada maxima

Overview of structure, function and integrated utilization of marine shell

Marine shell resources have received great attention from researchers owing to their unique merits such as high hardness, good toughness, corrosion resistance, high adsorption, and bioactivity. Restricted by the level of comprehensive utilization technology, the utilization rate of shells is extremely low, resulting in serious waste and pollution. The research shows that the unique brick-mud structure of shells makes them have diverse and good functional characteristics, which guides them to have great utilization potential in different fields. Hence, this review highlights the constitutive relationship between microstructure-function-application of shells (e.g., gastropods, cephalopods, and amniotes), and the comprehensive applications and development ideas in the fields of biomedicine, adsorption enrichment, pHotocatalysis, marine carbon sink, and environmental deicer. It is worth mentioning that marine shells are currently well developed in three areas: bone repair, health care and medicinal value, and drug carrier, which together promote the progress of biomedical field. In addition, an in-depth summary of the application of marine shells in the adsorption and purification of various impurities such as crude oil, heavy metal ions and dyes at low-cost and high efficiency is presented. Finally, by integrating thoughts and approaches from different applications, we are committed to providing new pathways for the excavation and future high-value of shell resources, clarifying the existing development stages and bottlenecks, promoting the development of related technology industries, and achieving the synergistic win-win situation of economic and environmental benefits.

Proteomic and Transcriptomic Responses Enable Clams to Correct the pH of Calcifying Fluids and Sustain Biomineralization in Acidified Environments

Seawater pH and carbonate saturation are predicted to decrease dramatically by the end of the century. This process, designated ocean acidification (OA), threatens economically and ecologically important marine calcifiers, including the northern quahog (Mercenaria mercenaria). While many studies have demonstrated the adverse impacts of OA on bivalves, much less is known about mechanisms of resilience and adaptive strategies. Here, we examined clam responses to OA by evaluating cellular (hemocyte activities) and molecular (high-throughput proteomics, RNASeq) changes in hemolymph and extrapallial fluid (EPF-the site of biomineralization located between the mantle and the shell) in M. mercenaria continuously exposed to acidified (pH ~7.3; pCO₂ ~2700 ppm) and normal conditions (pH ~8.1; pCO₂ ~600 ppm) for one year. The extracellular pH of EPF and hemolymph (~7.5) was significantly higher than that of the external acidified seawater (~7.3). Under OA conditions, granulocytes (a sub-population of hemocytes important for biomineralization) were able to increase intracellular pH (by 54% in EPF and 79% in hemolymph) and calcium content (by 56% in hemolymph). The increased pH of EPF and hemolymph from clams exposed to high pCO₂ was associated with the overexpression of genes (at both the mRNA and protein levels) related to biomineralization, acid-base balance, and calcium homeostasis, suggesting that clams can use corrective mechanisms to mitigate the negative impact of OA.

Organic Matrix and Secondary Metabolites in Nacre

Nacre, also called mother-of-pearl, is a naturally occurring biomineral, largely studied by chemists, structural biologists, and physicists to understand its outstanding and diverse properties. Nacre is constituted of aragonite nanograins surrounded by organic matrix, and it has been established that the organic matrix is responsible for initiating and guiding the biomineralization process. The first challenge to study the organic matrix of nacre lays in its separation from the biomineral. Several extraction methods have been developed so far. They are categorized as either strong (e.g., decalcification) or soft (e.g., water, ethanol) and they allow specific extractions of targeted compounds. The structure of the nacreous organic matrix is complex, and it provides interesting clues to describe the mineralization process. Proteins, sugars, lipids, peptides, and other molecules have been identified and their role in mineralization investigated. Moreover, the organic matrix of nacre has shown interesting properties for human health. Several studies are investigating its activity on bone mineralization and its properties for skin care. In this review, we focus on the organic constituents, as lipids, sugars, and small metabolites which are less studied since present in small quantities.

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.

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 novel matrix protein hic7 of hyriopsis cumingii participates in the formation of the shell and pearl

Shell matrix proteins have important roles in the biomineralization of shells. In this study, we isolated and identified a novel shell matrix protein gene, hic7, from the mussel Hyriopsis cumingii. The cDNA of hic7 was 459 bp long, including a 240-bp open reading frame. It encoded a 79 amino acid-long protein, with amino acids 1-19 constituting the signal peptide. The resulting hic7 is rich in cysteine (16.5%). After removing the signal peptide, the molecular weight was 8.85 kDa and the theoretical isoelectric point was 6.34, indicating that hic7 is a weakly acidic shell matrix protein. Hic7 is mainly expressed in the mantle tissue of H. cumingii. In situ hybridization showed hic7 signals at the edge and dorsal region of the mantle outer fold, indicating that it is related to the formation of the prismatic and nacreous layer of the shell. RNA interference indicated that when hic7 was inhibited by 80%, the crystal morphology of the prism and nacre layers of the shell were irregular and disordered. In addition, the expression of hic7 during the early development of the pearl sac indicated that it has an important role in the transformation of calcium carbonate crystals from a disordered to an orderly deposition pattern. These results suggest that matrix protein hic7 take part in constructing the framework of crystal nucleation and regulating the calcium carbonate crystal morphology of the nacreous and prismatic layers of shells and pearls.

Pearl Powder-An Emerging Material for Biomedical Applications: A Review

Pearl powder is a well-known traditional Chinese medicine for a variety of indications from beauty care to healthcare. While used for over a thousand years, there has yet to be an in-depth understanding and review in this area. The use of pearl powder is particularly growing in the biomedical area with various benefits reported due to the active ingredients within the pearl matrix itself. In this review, we focus on the emerging biomedical applications of pearl powder, touching on applications of pearl powder in wound healing, bone repairing, treatment of skin conditions, and other health indications.

Natural arrangement of fiber-like aragonites and its impact on mechanical behavior of mollusk shells: A review

During billions of years of evolution, creatures in nature have possessed nearly perfect structures and functions for survival. Multiscale structures in biological materials over several length scales play a pivotal role in achieving structural and functional integrity. Fiber, as a common principal structural element in nature, can be easily constructed in different ways, thus resulting in various natural structures. In this review, we summarized the decades of investigations on a typical biological structure constructed by fiber aragonites in mollusk shells. Crossed-lamellar structure, as one of the most widespread structures in mollusk shells, reconciles the strength-toughness trade-off dilemma successfully due to the presence of highly-hierarchical architectures. This distinctive structure includes several orders of sub-lamellae, and the different order lamellae present a cross-ply feature in one macro crossed-lamellar layer. When a mollusk shell has more than one macro-layer, the crossed-lamellar structure exhibits various forms of architectures including 0°/90°, 0°/90°/0° typical-sandwich, 15°/75°/0° quasi-sandwich, and 0°/90°/0°/90° arranged modes. The fracture resistance and the relevant toughening mechanisms are directly related to the highly-hierarchical crossed-lamellar structures on different length scales. This article is aimed to review the different arranged modes of crossed-lamellar structures existing in nature, with special attention to their impact on the mechanical behavior and salient toughening mechanisms over several length scales, for seeking the design guidelines for the fabrication of bio-inspired advanced engineering materials that are adaptive to different loading conditions.

Optimization of skeletal protein preparation for LC-MS/MS sequencing yields additional coral skeletal proteins in Stylophora pistillata

Stony corals generate their calcium carbonate exoskeleton in a highly controlled biomineralization process mediated by a variety of macromolecules including proteins. Fully identifying and classifying these proteins is crucial to understanding their role in exoskeleton formation, yet no optimal method to purify and characterize the full suite of extracted coral skeletal proteins has been established and hence their complete composition remains obscure. Here, we tested four skeletal protein purification protocols using acetone precipitation and ultrafiltration dialysis filters to present a comprehensive scleractinian coral skeletal proteome. We identified a total of 60 proteins in the coral skeleton, 44 of which were not present in previously published stony coral skeletal proteomes. Extracted protein purification protocols carried out in this study revealed that no one method captures all proteins and each protocol revealed a unique set of method-exclusive proteins. To better understand the general mechanism of skeletal protein transportation, we further examined the proteins’ gene ontology, transmembrane domains, and signal peptides. We found that transmembrane domain proteins and signal peptide secretion pathways, by themselves, could not explain the transportation of proteins to the skeleton. We therefore propose that some proteins are transported to the skeleton via non-traditional secretion pathways.

New insights into the spatial confinement mechanism of nucleation of biogenic aragonite crystals from bivalve nacre

Nacreous aragonite crystals nucleate on the margin of the underlying tablets: a spatial confinement mechanism.

Non-classical crystal growth on a hydrophobic substrate: learning from bivalve nacre

The hydrophobic substrate has an effect on the non-classical crystallization of nacreous aragonite crystals.

The osteoinductive effect of nano-nacre particles on MC-3T3 E1 preosteoblast through controlled release of water soluble matrix and calciumions

Prostheses and implants have been widely utilized in the orthopedic and dental fields. Nowadays, significant advances have been made in the structural and functional connection between living bone and prostheses, especially in the presence of compromised bone quantity/quality. Despite improvement in the treatment outcomes after augmentation, there are still challenges to meet the clinical demands due to limited materials available. In the current study, we investigated the effects of nano-nacre particles as an alternative material on stimulating bone cell differentiation and formation. Mouse osteoblastic cells (MC3T3-E1) were cultured on nano-nacre/type I collagen composite scaffold (NN-ICS) and type I collagen scaffold (ICS). Generated nano-nacre particles showed controlled release of protein and calcium for a period of 36 days. NN-ICS significantly contributed to the proliferation and differentiation of preosteoblasts compared to ICS controls. Our data showed that nano-nacre particles could serve as a candidate of bone substitution material, which potentially contributed to treatment outcomes in cases with compromised bone quality and/or quality.

Calcium Carbonate Skeletal Material Is Synthesized via Phase Transition of the Calcium Carbonate Cartilaginous Material

The formation mechanism of calcium carbonate (CC) skeletal tissues in biomineralization has remained poorly understood for a long time. Here, we propose an artificial CC biomineralization system equivalent to the natural one in terms of the primary physicochemical mechanism. Our system is constructed of a polymer gel and a CC solution unsaturated by a dissociated anionic polymer. The gel network consists of proton donor and proton acceptor polymers, which are analogues of polymers in the natural biomineralization system and have affinity for each other through hydrogen bonding interaction. Artificial biomineralization takes place within the polymer gel to produce a monolithic composite of the network and CC, whose powder X-ray diffraction pattern indicates calcite or calcite/vaterite. Scanning electron microscopy and energy-dispersive X-ray spectroscopy observation of the composite during the mineralization process revealed a two-phase structure (network/CC solid solution phase and CC hypercomplex gel phase). As artificial biomineralization proceeds, the solid phase grows in size at the cost of the gel phase as if the latter is substituted with the former, until the solid phase occupies the whole depth of the composite. These results suggest that the hypercomplex gel is the precursor of the resultant network/CC solid solution, and its discontinuous change is a phase transition to the solid solution. Despite minute differences in higher-order structures between our model system and the natural system, the fundamental structure of CC skeletal tissues in the latter can be interpreted as a network/CC solid solution, whereas that of CC cartilaginous tissues as a CC hypercomplex gel. Then, it can be deduced that, in biomineralization, the CC skeletal tissue is in principle formed via a phase transition of the CC cartilaginous tissue.

Induction of Osteogenic MC3T3-E1 Cell Differentiation by Nacre and Flesh Lipids of Tunisian Pinctada radiata

The flesh of the Pinctada radiata pearl oyster from coastal Tunisia is considered as a high source of n-3 and n-6 and its shell nacre layer is a promising osteogenic biomaterial. Fatty acid (FA) analysis showed that the major components found in total FA (TFA) were 14:0, 16:0, and 18:0 saturated FA (SFA); 16:1, 18:1, and 20:1 monoenoic FA; 20:4n-6 (ARA), 22:5n-3 (DPA). Characteristically high levels of 20:5n-3 (EPA) and 22:6n-3 (DHA) (6.53-89.75 mg/100 g TFA) polyunsaturated FA (PUFA) were found, respectively, in the TFA of nacre and flesh. Evaluated the effects in vitro of lipids extracted from nacre (Ln) and from flesh (Lc) of P. radiata on growth and the differentiation of osteoblasts. Cytotoxicity tests (3-(4, 5-dimethylthiazolyl-2)-2, 5-diphenyltetrazolium bromide [MTT] and lactic acid dehydrogenase c [LDH]) demonstrated that both extracts are nontoxic. Alizarin Red staining was used in an osteoblast differentiation model using the osteoblast MC3T3-E1 cell line. It showed that the FA of both extracts induced osteoblast differentiation leading to mineralization. Reverse transcription-polymerase chain reaction (RT-PCR) showed a significantly higher expression of osteocalcin (Bglap) and runt-related transcription (Runx2) in MC3T3-E1 cells in the presence of Ln. No difference of osteopontin (Spp1) and Collagen type I (Col1a1) genes compared to the control was observed. In conclusion, these results supported, obtained from our in vitro experimental model used, the interest/potential of lipids extracted from nacre and P. radiata flesh to stimulate bone formation.

Composite Materials Design: Biomineralization Proteins and the Guided Assembly and Organization of Biomineral Nanoparticles

There has been much discussion of the role of proteins in the calcium carbonate biomineralization process, particularly with regard to nucleation, amorphous stabilization/transformation, and polymorph selection. However, there has been little if any discussion of the potential role that proteins might play in another important process: the guided assembly and organization of mineral nanoparticles into higher-ordered structures such as mesocrystals. This review discusses particle attachment theory and recent evidence of mineral-associated proteins forming hydrogels that assemble and organize mineral clusters into crystalline phase. From this discussion we postulate a mechanism by which biomineralization protein hydrogel aggregation assists in mineral nanoparticle assembly and organization within calcium carbonate skeletal elements and discuss potentials ways for harnessing this process in materials design.

Biomacromolecules within bivalve shells: Is chitin abundant?

Bivalve shells are inorganic-organic nanocomposites whose material properties outperform their purely inorganic mineral counterparts. Most typically the inorganic phase is a polymorph of CaCO₃, while the organic phase contains biopolymers which have been presumed to be chitin and/or proteins. Identifying the biopolymer phase is therefore a crucial step in improving our understanding of design principles relevant to biominerals. In this work we study seven shells; four are examples of nacroprismatic shells (Alathyria jacksoni, Pinctada maxima, Hyriopsis cumingii and Cucumerunio novaehollandiae), one homogeneous (Arctica islandica), and two are crossed lamellar (Callista kingii, Tridacna gigas). Both intact shells, their organic extracts as isolated after decalcification in acid, and the periostracum overlay have been studied by solid-state CP-MAS NMR, FTIR, SEM and chemical analysis. In none of the shells examined in this work do we find a significant contribution to the organic fraction from chitin or its derivatives despite popular models of bivalve biomineralization which assume abundant chitin in the organic fraction of mollusk bivalve shells. In each of the nacroprismatic extracts the ¹³C NMR spectra represent similar proteinaceous material, Ala and Gly-rich and primarily organized as β-sheets. A different, yet highly conserved protein was found in the periostracum covering each of the three nacreous shells studied. The Arctica islandica shells with homogeneous microstructure contained proteins which do not appear to be silk-like, while in the crossed lamellar shells we extracted too little organic matter to characterize. STATEMENT OF SIGNIFICANCE: Hydrophobic macromolecules are structural components within the calcareous inorganic matrix of bivalve shells and are responsible for enhanced materials properties of the biominerals. Prevalent models suggest that chitin is such major hydrophobic component. Contrary to that we show that chitin is rare within the hydrophobic biopolymers which primarily consist of proteinaceous matter with structural motifs as silk-like β-sheets, or others yet to be determined. Recognizing that diverse proteinaceous motifs, devoid of abundant chitin, can yield the optimized mechanical properties of bivalve shells is critical both to understand the mechanistic pathways by which they regulate biomineralization and for the design of novel bioinspired materials.

Cloning, characterization and functional analysis of an Alveoline-like protein in the shell of Pinctada fucata

Shell matrix proteins (SMPs) have important functions in biomineralization. In the past decades, the roles of SMPs were gradually revealed. In 2015, our group identified 72 unique SMPs in Pinctada fucata, among which Alveoline-like (Alv) protein was reported to have homologous genes in Pinctada maxima and Pinctada margaritifera. In this study, the full-length cDNA sequence of Alv and the functional analysis of Alv protein during shell formation were explored. The deduced protein (Alv), which has a molecular mass of 24.9 kDa and an isoelectric point of 11.34, was characterized, and the functional analyses was explored in vivo and in vitro. The Alv gene has high expression in mantle and could response to notching damage. The functional inhibition of Alv protein in vivo by injecting recombinant Alv (rAlv) antibodies destroyed prism structure but accelerated nacre growth. Western blot and immunofluorescence staining showed that native Alv exists in the EDTA-insoluble matrix of both prismatic and nacreous layers and has different distribution patterns in the inner or outer prismatic layer. Taken together, the characterization and functional analyses of matrix protein Alv could expand our understanding of basic matrix proteins and their functions during shell formation.

Regulation of Extracellular Matrix Synthesis by Shell Extracts from the Marine Bivalve Pecten maximus in Human Articular Chondrocytes- Application for Cartilage Engineering

The shells of the bivalve mollusks are organo-mineral structures predominantly composed of calcium carbonate, but also of a minor organic matrix, a mixture of proteins, glycoproteins, and polysaccharides. These proteins are involved in mineral deposition and, more generally, in the spatial organization of the shell crystallites in well-defined microstructures. In this work, we extracted different organic shell extracts (acid-soluble matrix, acid-insoluble matrix, water-soluble matrix, guanidine HCl/EDTA-extracted matrix, referred as ASM, AIM, WSM, and EDTAM, respectively) from the shell of the scallop Pecten maximus and studied their biological activities on human articular chondrocytes (HACs). We found that these extracts differentially modulate the biological activities of HACs, depending on the type of extraction and the concentration used. Furthermore, we showed that, unlike ASM and AIM, WSM promotes maintenance of the chondrocyte phenotype in monolayer culture. WSM increased the expression of chondrocyte-specific markers (aggrecan and type II collagen), without enhancing that of the main chondrocyte dedifferentiation marker (type I collagen). We also demonstrated that WSM could favor redifferentiation of chondrocyte in collagen sponge scaffold in hypoxia. Thus, this study suggests that the organic matrix of Pecten maximus, particularly WSM, may contain interesting molecules with chondrogenic effects. Our research emphasizes the potential use of WSM of Pecten maximus for cell therapy of cartilage.

The pearl oyster Pinctada fucata martensii genome and multi-omic analyses provide insights into biomineralization

Nacre, the iridescent material found in pearls and shells of molluscs, is formed through an extraordinary process of matrix-assisted biomineralization. Despite recent advances, many aspects of the biomineralization process and its evolutionary origin remain unknown. The pearl oyster Pinctada fucata martensii is a well-known master of biomineralization, but the molecular mechanisms that underlie its production of shells and pearls are not fully understood. We sequenced the highly polymorphic genome of the pearl oyster and conducted multi-omic and biochemical studies to probe nacre formation. We identified a large set of novel proteins participating in matrix-framework formation, many in expanded families, including components similar to that found in vertebrate bones such as collagen-related VWA-containing proteins, chondroitin sulfotransferases, and regulatory elements. Considering that there are only collagen-based matrices in vertebrate bones and chitin-based matrices in most invertebrate skeletons, the presence of both chitin and elements of collagen-based matrices in nacre suggests that elements of chitin- and collagen-based matrices have deep roots and might be part of an ancient biomineralizing matrix. Our results expand the current shell matrix-framework model and provide new insights into the evolution of diverse biomineralization systems.

Architecture of crossed-lamellar bivalve shells: the southern giant clam (Tridacna derasa, Röding, 1798)

Tridacna derasa shells show a crossed lamellar microstructure consisting of three hierarchical lamellar structural orders. The mineral part is intimately intergrown with 0.9 wt% organics, namely polysaccharides, glycosylated and unglycosylated proteins and lipids, identified by Fourier transform infrared spectrometry. Transmission electron microscopy shows nanometre-sized grains with irregular grain boundaries and abundant voids. Twinning is observed across all spatial scales and results in a spread of the crystal orientation angles. Electron backscatter diffraction analysis shows a strong fibre texture with the [001] axes of aragonite aligned radially to the shell surface. The aragonitic [100] and [010] axes are oriented randomly around [001]. The random orientation of anisotropic crystallographic directions in this plane reduces anisotropy of the Young's modulus and adds to the optimization of mechanical properties of bivalve shells.

Retrosynthesis of CaCO3 via amorphous precursor particles using gastroliths of the Red Claw lobster (Cherax quadricarinatus)

Gastroliths are highly calcified structures formed in the cardiac stomach wall of crustaceans for the temporary storage of amorphous CaCO₃ (ACC). The gastrolithic ACC is stabilized by the presence of biomolecules, and represents a novel model for research into biomineralization. For the first time, an in vitro biomimetic retrosynthesis of scaffolds of gastrolithic matrices with CaCO₃ is presented. With the help of synthetic polyacrylic (PAA) and phytic (PA) acids, amorphous precursor particles were stabilized in double (DD) and gas (GD) diffusion crystallization assays. The presence of these synthetic molecules as efficient inhibitors of nucleation and growth of CaCO₃, and the use of biological gastrolith scaffolds as confined reaction environments determined the kinetics of crystallization, and controlled the morphogenesis of CaCO₃. The formation of ACC particles was demonstrated and their crystallization was followed by light microscopy, scanning and transmission electron microscopy, and electron diffraction.

Shell extracts of the edible mussel and oyster induce an enhancement of the catabolic pathway of human skin fibroblasts, in vitro

Mollusc shells are composed of more than 95% calcium carbonate and less than 5% organic matrix consisting mostly of proteins, glycoproteins and polysaccharides. In this study, we investigated the effects of matrix macromolecular components extracted from the shells of two edible molluscs of economic interest, i.e., the blue mussel Mytilus edulis and the Pacific oyster Crassostrea gigas. The potential biological activities of these organic molecules were analysed on human dermal fibroblasts in primary culture. Our results demonstrate that shell extracts of the two studied molluscs modulate the metabolic activities of the cells. In addition, the extracts caused a decrease of type I collagen and a concomitant increase of active MMP-1, both at the mRNA and the protein levels. Therefore, our results suggest that shell extracts from M. edulis and C. gigas contain molecules that promote the catabolic pathway of human dermal fibroblasts. This work emphasises the potential use of these shell matrices in the context of anti-fibrotic strategies, particularly against scleroderma. More generally, it stresses the usefulness to valorise bivalve shells that are coproducts of shellfish farming activity.

Expansion for the Brachylophosaurus canadensis Collagen I Sequence and Additional Evidence of the Preservation of Cretaceous Protein

Sequence data from biomolecules such as DNA and proteins, which provide critical information for evolutionary studies, have been assumed to be forever outside the reach of dinosaur paleontology. Proteins, which are predicted to have greater longevity than DNA, have been recovered from two nonavian dinosaurs, but these results remain controversial. For proteomic data derived from extinct Mesozoic organisms to reach their greatest potential for investigating questions of phylogeny and paleobiology, it must be shown that peptide sequences can be reliably and reproducibly obtained from fossils and that fragmentary sequences for ancient proteins can be increasingly expanded. To test the hypothesis that peptides can be repeatedly detected and validated from fossil tissues many millions of years old, we applied updated extraction methodology, high-resolution mass spectrometry, and bioinformatics analyses on a Brachylophosaurus canadensis specimen (MOR 2598) from which collagen I peptides were recovered in 2009. We recovered eight peptide sequences of collagen I: two identical to peptides recovered in 2009 and six new peptides. Phylogenetic analyses place the recovered sequences within basal archosauria. When only the new sequences are considered, B. canadensis is grouped more closely to crocodylians, but when all sequences (current and those reported in 2009) are analyzed, B. canadensis is placed more closely to basal birds. The data robustly support the hypothesis of an endogenous origin for these peptides, confirm the idea that peptides can survive in specimens tens of millions of years old, and bolster the validity of the 2009 study. Furthermore, the new data expand the coverage of B. canadensis collagen I (a 33.6% increase in collagen I alpha 1 and 116.7% in alpha 2). Finally, this study demonstrates the importance of reexamining previously studied specimens with updated methods and instrumentation, as we obtained roughly the same amount of sequence data as the previous study with substantially less sample material. Data are available via ProteomeXchange with identifier PXD005087.

An Efficient Method for Co-purification of Eggshell Matrix Proteins OC-17, OC-116, and OCX-36

In this study, we improved the eggshell-membrane separation process by separating the shell and membrane with EDTA solution, evaluating effects of three different extraction solutions (acetic acid, EDTA, and phosphate solution), and co-purifying multiple eggshell proteins with two successive ion-exchange chromatography procedures (CM Sepharose Fast Flow and DEAE Sepharose Fast Flow). The recovery and residual rates of eggshell and membrane separated by the modified method with added EDTA solution were 93.88%, 91.15% and 1.01%, 2.87%, respectively. Ovocleidin-116 (OC-116) and ovocalyxin-36 (OCX-36) were obtained by loading 50 mM Na-Hepes, pH 7.5, 2 mM DTT and 350 mM NaCl buffer onto the DEAE-FF column at a flow rate of 1 mL/min, ovocleidin-17 (OC-17) was obtained by loading 100 mM NaCl, 50 mM Tris, pH 8.0 on the CM-FF column at a flow rate of 0.5 mL/min. The purities of OCX-36, OC-17 and OC-116 were 96.82%, 80.15% and 73.22%, and the recovery rates were 55.27%, 53.38% and 36.34%, respectively. Antibacterial activity test suggested that phosphate solution extract exhibited significantly higher activity against the tested bacterial strains than the acetic acid or EDTA extract, probably due to more types of proteins in the extract. These results demonstrate that this separation method is feasible and efficient.

Mineralization and non-ideality: on nature's foundry

Understanding how ions, ion-clusters and particles behave in non-ideal environments is a fundamental question concerning planetary to atomic scales. For biomineralization phenomena wherein diverse inorganic and organic ingredients are present in biological media, attributing biomaterial composition and structure to the chemistry of singular additives may not provide a holistic view of the underlying mechanisms. Therefore, in this review, we specifically address the consequences of physico-chemical non-ideality on mineral formation. Influences of different forms of non-ideality such as macromolecular crowding, confinement and liquid-like organic phases on mineral nucleation and crystallization in biological environments are presented. Novel prospects for the additive-controlled nucleation and crystallization are accessible from this biophysical view. In this manner, we show that non-ideal conditions significantly affect the form, structure and composition of biogenic and biomimetic minerals.

Bone protein "extractomics": comparing the efficiency of bone protein extractions of Gallus gallus in tandem mass spectrometry, with an eye towards paleoproteomics

Proteomic studies of bone require specialized extraction protocols to demineralize and solubilize proteins from within the bone matrix. Although various protocols exist for bone protein recovery, little is known about how discrete steps in each protocol affect the subset of the bone proteome recovered by mass spectrometry (MS) analyses. Characterizing these different “extractomes” will provide critical data for development of novel and more efficient protein extraction methodologies for fossils. Here, we analyze 22 unique sub-extractions of chicken bone and directly compare individual extraction components for their total protein yield and diversity and coverage of bone proteins identified by MS. We extracted proteins using different combinations and ratios of demineralizing reagents, protein-solubilizing reagents, and post-extraction buffer removal methods, then evaluated tryptic digests from 20 µg aliquots of each fraction by tandem MS/MS on a 12T FT-ICR mass spectrometer. We compared total numbers of peptide spectral matches, peptides, and proteins identified from each fraction, the redundancy of protein identifications between discrete steps of extraction methods, and the sequence coverage obtained for select, abundant proteins. Although both alpha chains of collagen I (the most abundant protein in bone) were found in all fractions, other collagenous and non-collagenous proteins (e.g., apolipoprotein, osteonectin, hemoglobin) were differentially identified. We found that when a standardized amount of extracted proteins was analyzed, extraction steps that yielded the most protein (by weight) from bone were often not the ones that produced the greatest diversity of bone proteins, or the highest degree of protein coverage. Generally, the highest degrees of diversity and coverage were obtained from demineralization fractions, and the proteins found in the subsequent solubilization fractions were highly redundant with those in the previous fraction. Based on these data, we identify future directions and parameters to consider (e.g., proteins targeted, amount of sample required) when applying discrete parts of these protocols to fossils.

The Widespread Prevalence and Functional Significance of Silk-Like Structural Proteins in Metazoan Biological Materials

In nature, numerous mechanisms have evolved by which organisms fabricate biological structures with an impressive array of physical characteristics. Some examples of metazoan biological materials include the highly elastic byssal threads by which bivalves attach themselves to rocks, biomineralized structures that form the skeletons of various animals, and spider silks that are renowned for their exceptional strength and elasticity. The remarkable properties of silks, which are perhaps the best studied biological materials, are the result of the highly repetitive, modular, and biased amino acid composition of the proteins that compose them. Interestingly, similar levels of modularity/repetitiveness and similar bias in amino acid compositions have been reported in proteins that are components of structural materials in other organisms, however the exact nature and extent of this similarity, and its functional and evolutionary relevance, is unknown. Here, we investigate this similarity and use sequence features common to silks and other known structural proteins to develop a bioinformatics-based method to identify similar proteins from large-scale transcriptome and whole-genome datasets. We show that a large number of proteins identified using this method have roles in biological material formation throughout the animal kingdom. Despite the similarity in sequence characteristics, most of the silk-like structural proteins (SLSPs) identified in this study appear to have evolved independently and are restricted to a particular animal lineage. Although the exact function of many of these SLSPs is unknown, the apparent independent evolution of proteins with similar sequence characteristics in divergent lineages suggests that these features are important for the assembly of biological materials. The identification of these characteristics enable the generation of testable hypotheses regarding the mechanisms by which these proteins assemble and direct the construction of biological materials with diverse morphologies. The SilkSlider predictor software developed here is available at https://github.com/wwood/SilkSlider.

Principles of calcium-based biomineralization

The chapter provides some basic information on the formation principles of calcium carbonate in biological systems in marine environment in the point of view of materials science in order to provide strategies for biomimetic design and preparation of new functional materials. Many researchers try to explain the principles of biomineralization and get some valuable conclusions. This chapter introduces some calcium-based biominerals in aquatic organisms which mainly include calcium carbonate and calcium phosphate. Then it gives a presentation of the hierarchical structure of calcium carbonate-based and calcium phosphate-based biominerals, e.g., mollusc shell, pearl, carp otolith, tooth, and bone. Moreover, the chapter explains the principles of calcium carbonate mineralization from the aspects of the effects of additives and templates; it also gives some explanations to the principles of calcium phosphate mineralization.

Austromegabalanus psittacus barnacle shell structure and proteoglycan localization and functionality

Comparative analyzes of biomineralization models have being crucial for the understanding of the functional properties of biominerals and the elucidation of the processes through which biomacromolecules control the synthesis and structural organization of inorganic mineral-based biomaterials. Among calcium carbonate-containing bioceramics, egg, mollusk and echinoderm shells, and crustacean carapaces, have being fairly well characterized. However, Thoraceca barnacles, although being crustacea, showing molting cycle, build a quite stable and heavily mineralized shell that completely surround the animal, which is for life firmly cemented to the substratum. This makes barnacles an interesting model for studying processes of biomineralization. Here we studied the main microstructural and ultrastructural features of Austromegabalanus psittacus barnacle shell, characterize the occurrence of specific proteoglycans (keratan-, dermatan- and chondroitin-6-sulfate proteoglycans) in different soluble and insoluble organic fractions extracted from the shell, and tested them for their ability to crystallize calcium carbonate in vitro. Our results indicate that, in the barnacle model, proteoglycans are good candidates for the modification of the calcite crystal morphology, although the cooperative effect of some additional proteins in the shell could not be excluded.

Intracrystalline inclusions within single crystalline hosts: from biomineralization to bio-inspired crystal growth

A review of the inclusion of organic matter within single crystalline hosts: from biogenic minerals to bio-inspired nanohybrid single crystal composites.

Biomineralization of Schlumbergerella floresiana, a significant carbonate-producing benthic foraminifer

Most foraminifera that produce a shell are efficient biomineralizers. We analyzed the calcitic shell of the large tropical benthic foraminifer Schlumbergerella floresiana. We found a suite of macromolecules containing many charged and polar amino acids and glycine that are also abundant in biomineralization proteins of other phyla. As neither genomic nor transcriptomic data are available for foraminiferal biomineralization yet, de novo-generated sequences, obtained from organic matrices submitted to ms blast database search, led to the characterization of 156 peptides. Very few homologous proteins were matched in the proteomic database, implying that the peptides are derived from unknown proteins present in the foraminiferal organic matrices. The amino acid distribution of these peptides was queried against the uniprot database and the mollusk uniprot database for comparison. The mollusks compose a well-studied phylum that yield a large variety of biomineralization proteins. These results showed that proteins extracted from S. floresiana shells contained sequences enriched with glycine, alanine, and proline, making a set of residues that provided a signature unique to foraminifera. Three of the de novo peptides exhibited sequence similarities to peptides found in proteins such as pre-collagen-P and a group of P-type ATPases including a calcium-transporting ATPase. Surprisingly, the peptide that was most similar to the collagen-like protein was a glycine-rich peptide reported from the test and spine proteome of sea urchin. The molecules, identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry analyses, included acid-soluble N-glycoproteins with its sugar moieties represented by high-mannose-type glycans and carbohydrates. Describing the nature of the proteins, and associated molecules in the skeletal structure of living foraminifera, can elucidate the biomineralization mechanisms of these major carbonate producers in marine ecosystems. As fossil foraminifera provide important paleoenvironmental and paleoclimatic information, a better understanding of biomineralization in these organisms will have far-reaching impacts.

Shell extracts from the marine bivalve Pecten maximus regulate the synthesis of extracellular matrix in primary cultured human skin fibroblasts

Mollusc shells are composed of more than 95% calcium carbonate and less than 5% of an organic matrix consisting mostly of proteins, glycoproteins and polysaccharides. Previous studies have elucidated the biological activities of the shell matrices from bivalve molluscs on skin, especially on the expression of the extracellular matrix components of fibroblasts. In this work, we have investigated the potential biological activities of shell matrix components extracted from the shell of the scallop Pecten maximus on human fibroblasts in primary culture. Firstly, we demonstrated that shell matrix components had different effects on general cellular activities. Secondly, we have shown that the shell matrix components stimulate the synthesis of type I and III collagens, as well as that of sulphated GAGs. The increased expression of type I collagen is likely mediated by the recruitment of transactivating factors (Sp1, Sp3 and human c-Krox) in the −112/−61 bp COL1A1 promoter region. Finally, contrarily to what was obtained in previous works, we demonstrated that the scallop shell extracts have only a small effect on cell migration during in vitro wound tests and have no effect on cell proliferation. Thus, our research emphasizes the potential use of shell matrix of Pecten maximus for dermo-cosmetic applications.

Shotgun proteomics analysis of proliferating STRO-1-positive human dental pulp cell after exposure to nacreous water-soluble matrix

INTRODUCTION

For dental treatment, dentin regeneration is required after a tooth injury with dental pulp exposure. The effects of the water-soluble matrix (WSM) extracted from the nacreous layer of the bivalve Pinctada maxima on human dental pulp cells in vitro were challenging and useful for clinical application.

MATERIAL AND METHODS

The biological activity of the STRO-1-positive human dental pulp cells in response to WSM compared to Dulbecco's modified Eagle medium (DMEM) as a normal control was monitored. The cell survival rate was analyzed by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Proteomic profiles among inducers and noninducers with time dependency were compared by using sodium dodecyl sulfate-polyacrylamide gel electrophoresis combined with liquid chromatography-tandem mass spectrometry (GeLC-MS/MS).

RESULTS

The human dental pulp cells cultured in nacreous WSM exhibited higher relative cell viability than those in DMEM with similar morphological appearance. Significant changes were found in the relative abundance of 44 proteins in cells after exposure to WSM for 2 weeks. They play a role in cell adhesion, cell proliferation, metabolic process, signal transduction, stress response, transcription, translation, and transport.

CONCLUSION

These results indicate that WSM of P. maxima has the ability to induce proliferation of human dental pulp cells.

CLINICAL RELEVANCE

This finding initiated the study to evaluate the suitability of nacre as biomaterial for dentistry.

Change in the chicken eggshell cuticle with hen age and egg freshness

For a fuller understanding of the functionality of the eggshell cuticle, we conducted a detailed study using a wide array of analytical techniques (scanning and transmission microscopy), energy dispersive x-rays, and attenuated total reflection-Fourier transform infrared spectroscopy to analyze the structure, morphology, and chemical composition of this organic coating. This study shows that the cuticle has a compositional gradation with an outer part richer in proteins and an inner part richer in sulfated polysaccharides and phosphates. It also shown that the cuticle composition, thickness, and degree of coverage are highly dependent on hen age and egg freshness. During the course of the first laying year, the thickness and degree of glycosylation of the cuticle decreases with hen age, and at the end of the laying cycle, the cuticle is significantly depleted in lipids. There are also well-defined compositional changes in the cuticle of freshly laid eggs as time passes and there is a notable increase in the permeability of the eggshell after 24 h due to cuticle drying. We discuss how these changes in the cuticle can affect the food safety of eggs in relation to the risk of trans-shell contamination by bacteria (i.e., Salmonellosis).

A novel acidic matrix protein, PfN44, stabilizes magnesium calcite to inhibit the crystallization of aragonite

Magnesium is widely used to control calcium carbonate deposition in the shell of pearl oysters. Matrix proteins in the shell are responsible for nucleation and growth of calcium carbonate crystals. However, there is no direct evidence supporting a connection between matrix proteins and magnesium. Here, we identified a novel acidic matrix protein named PfN44 that affected aragonite formation in the shell of the pearl oyster Pinctada fucata. Using immunogold labeling assays, we found PfN44 in both the nacreous and prismatic layers. In shell repair, PfN44 was repressed, whereas other matrix proteins were up-regulated. Disturbing the function of PfN44 by RNAi led to the deposition of porous nacreous tablets with overgrowth of crystals in the nacreous layer. By in vitro circular dichroism spectra and fluorescence quenching, we found that PfN44 bound to both calcium and magnesium with a stronger affinity for magnesium. During in vitro calcium carbonate crystallization and calcification of amorphous calcium carbonate, PfN44 regulated the magnesium content of crystalline carbonate polymorphs and stabilized magnesium calcite to inhibit aragonite deposition. Taken together, our results suggested that by stabilizing magnesium calcite to inhibit aragonite deposition, PfN44 participated in P. fucata shell formation. These observations extend our understanding of the connections between matrix proteins and magnesium.

In situ studies of nanoscale electromechanical behavior of nacre under flexural stresses using band excitation PFM

In this paper, we have studied the electromechanical coupling behaviors of nacre under non-destructive flexural stresses. Band excitation piezoresponse force microscopy is used as the primary tool to characterize the piezoelectric properties of nacre. This method can differentiate various constituents in nacre at the nanoscale and track their in situ responses under tensile and compressive stresses. The local ferroelectric hysteresis behaviors of nacre are also studied. Based on the hysteresis loops observed under different stress states, various phenomena, including the stress-induced internal field and energy loss, are revealed in this study.

What is the difference in organic matrix of aragonite vs. vaterite polymorph in natural shell and pearl? Study of the pearl-forming freshwater bivalve mollusc Hyriopsis cumingii

Aragonite pearl, vaterite pearl and shell nacre of the freshwater mollusc Hyriopsis cumingii (Zhejiang province, China) were chosen to analyze microstructure and organic composition in the different habits of calcium carbonate. SEM and TEM were used to reveal the microstructure and mineralogical phase. We found that tablets in vaterite exhibited more irregular texture and were packaged with more organic matrices than in aragonite forms. Then a peculiar method was introduced to extract water soluble matrix (WSM), acid soluble matrix (ASM) and acid insoluble matrix (AIM) from the three samples, and biochemical analysis of these organic matrixes involved in crystal formation and polymorph selection was carried out. High performance liquid chromatography (HPLC) confirms the hydrophobic pattern of the organic matrix intermingled with mineral, the opposite of the early mobilizable water soluble fraction. Amino acid composition confirms hydrophobic residues as major components of all the extracts, but it reveals an imbalance in acidic residues rates in WSM vs. ASM and in aragonite vs. vaterite. Electrophoresis gives evidence for signatures in proteins with a 140 kDa material specific for aragonite in WSM. Conversely all ASM extracts reveal the presence of about 55 kDa components, including a discrete band in vaterite extract.

Proteomic strategy for identifying mollusc shell proteins using mild chemical degradation and trypsin digestion of insoluble organic shell matrix: a pilot study on Haliotis tuberculata

A successful strategy for the identification of shell proteins is based on proteomic analyses where soluble and insoluble fractions isolated from organic shell matrix are digested with trypsin with the aim of generating peptides, which are used to identify novel shell proteins contained in databases. However, using trypsin as a sole degradative agent is limited by the enzyme's cleavage specificity and is dependent upon the occurrence of lysine and arginine in the shell protein sequence. To bypass this limitation, we investigated the ability of trifluoroacetic acid (TFA), a low-specificity chemical degradative agent, to generate clusters of analyzable peptides from organic shell matrix, suitable for database annotation. Acetic acid-insoluble fractions from Haliotis tuberculata shell were processed by trypsin followed by TFA digestion. The hydrolysates were used to annotate an expressed sequence tag library constructed from the mantle tissue of Haliotis asinina, a tropical abalone species. The characterization of sequences with repeat motifs featured in some of the shell matrix proteins benefited from TFA-induced serial cutting, which can result in peptide ladder series. Using the degradative specificities of TFA and trypsin, we were able to identify five novel shell proteins. This pilot study indicates that a mild chemical digestion of organic shell matrix combined with trypsin generates peptides suitable for proteomic analysis for better characterization of mollusc shell matrix proteins.

Spatial analysis of biomineralization associated gene expression from the mantle organ of the pearl oyster Pinctada maxima

BACKGROUND

Biomineralization is a process encompassing all mineral containing tissues produced within an organism. One of the most dynamic examples of this process is the formation of the mollusk shell, comprising a variety of crystal phases and microstructures. The organic component incorporated within the shell is said to dictate this architecture. However general understanding of how this process is achieved remains ambiguous. The mantle is a conserved organ involved in shell formation throughout molluscs. Specifically the mantle is thought to be responsible for secreting the protein component of the shell. This study employs molecular approaches to determine the spatial expression of genes within the mantle tissue to further the elucidation of the shell biomineralization.

RESULTS

A microarray platform was custom generated (PmaxArray 1.0) from the pearl oyster Pinctada maxima. PmaxArray 1.0 consists of 4992 expressed sequence tags (ESTs) originating from mantle tissue. This microarray was used to analyze the spatial expression of ESTs throughout the mantle organ. The mantle was dissected into five discrete regions and analyzed for differential gene expression with PmaxArray 1.0. Over 2000 ESTs were determined to be differentially expressed among the tissue sections, identifying five major expression regions. In situ hybridization validated and further localized the expression for a subset of these ESTs. Comparative sequence similarity analysis of these ESTs revealed a number of the transcripts were novel while others showed significant sequence similarities to previously characterized shell related genes.

CONCLUSIONS

This investigation has mapped the spatial distribution for over 2000 ESTs present on PmaxArray 1.0 with reference to specific locations of the mantle. Expression profile clusters have indicated at least five unique functioning zones in the mantle. Three of these zones are likely involved in shell related activities including formation of nacre, periostracum and calcitic prismatic microstructure. A number of novel and known transcripts have been identified from these clusters. The development of PmaxArray 1.0, and the spatial map of its ESTs expression in the mantle has begun characterizing the molecular mechanisms linking the organics and inorganics of the molluscan shell.

Metals affect the structure and activity of human plasminogen activator inhibitor-1. II. Binding affinity and conformational changes

Human plasminogen activator inhibitor type 1 (PAI-1) is a serine protease inhibitor with a metastable active conformation. The lifespan of the active form of PAI-1 is modulated via interaction with the plasma protein, vitronectin, and various metal ions. These metal ions fall into two categories: Type I metals, including calcium, magnesium, and manganese, stabilize PAI-1 in the absence of vitronectin, whereas Type II metals, including cobalt, copper, and nickel, destabilize PAI-1 in the absence of vitronectin, but stabilize PAI-1 in its presence. To provide a mechanistic basis for understanding the unusual modulation of PAI-1 structure and activity, the binding characteristics and conformational effects of these two types of metals were further evaluated. Steady-state binding measurements using surface plasmon resonance indicated that both active and latent PAI-1 exhibit a dissociation constant in the low micromolar range for binding to immobilized nickel. Stopped-flow measurements of approach-to-equilibrium changes in intrinsic protein fluorescence indicated that the Type I and Type II metals bind in different modes that induce distinct conformational effects on PAI-1. Changes in the observed rate constants with varying concentrations of metal allowed accurate determination of binding affinities for cobalt, nickel, and copper, yielding dissociation constants of ∼40, 30, and 0.09 μM, respectively. Competition experiments that tested effects on PAI-1 stability were consistent with these measurements of affinity and indicate that copper binds tightly to PAI-1.