Characterization of the proteins comprising the integral matrix of Strongylocentrotus purpuratus embryonic spicules

Ocean Warming Amplifies the Effects of Ocean Acidification on Skeletal Mineralogy and Microstructure in the Asterinid Starfish Aquilonastra yairi

Ocean acidification and ocean warming compromise the capacity of calcifying marine organisms to generate and maintain their skeletons. While many marine calcifying organisms precipitate low-Mg calcite or aragonite, the skeleton of echinoderms consists of more soluble Mg-calcite. To assess the impact of exposure to elevated temperature and increased pCO2 on the skeleton of echinoderms, in particular the mineralogy and microstructure, the starfish Aquilonastra yairi (Echinodermata: Asteroidea) was exposed for 90 days to simulated ocean warming (27 °C and 32 °C) and ocean acidification (455 µatm, 1052 µatm, 2066 µatm) conditions. The results indicate that temperature is the major factor controlling the skeletal Mg (Mg/Ca ratio and Mgnorm ratio), but not for skeletal Sr (Sr/Ca ratio and Srnorm ratio) and skeletal Ca (Canorm ratio) in A. yairi. Nevertheless, inter-individual variability in skeletal Sr and Ca ratios increased with higher temperature. Elevated pCO2 did not induce any statistically significant element alterations of the skeleton in all treatments over the incubation time, but increased pCO2 concentrations might possess an indirect effect on skeletal mineral ratio alteration. The influence of increased pCO2 was more relevant than that of increased temperature on skeletal microstructures. pCO2 as a sole stressor caused alterations on stereom structure and degradation on the skeletal structure of A. yairi, whereas temperature did not; however, skeletons exposed to elevated pCO2 and high temperature show a strongly altered skeleton structure compared to ambient temperature. These results indicate that ocean warming might exacerbate the skeletal maintaining mechanisms of the starfish in a high pCO2 environment and could potentially modify the morphology and functions of the starfish skeleton.

The Evolution of Biomineralization through the Co-Option of Organic Scaffold Forming Networks

Biomineralization is the process in which organisms use minerals to generate hard structures like teeth, skeletons and shells. Biomineralization is proposed to have evolved independently in different phyla through the co-option of pre-existing developmental programs. Comparing the gene regulatory networks (GRNs) that drive biomineralization in different species could illuminate the molecular evolution of biomineralization. Skeletogenesis in the sea urchin embryo was extensively studied and the underlying GRN shows high conservation within echinoderms, larval and adult skeletogenesis. The organic scaffold in which the calcite skeletal elements form in echinoderms is a tubular compartment generated by the syncytial skeletogenic cells. This is strictly different than the organic cartilaginous scaffold that vertebrates mineralize with hydroxyapatite to make their bones. Here I compare the GRNs that drive biomineralization and tubulogenesis in echinoderms and in vertebrates. The GRN that drives skeletogenesis in the sea urchin embryo shows little similarity to the GRN that drives bone formation and high resemblance to the GRN that drives vertebrates’ vascular tubulogenesis. On the other hand, vertebrates’ bone-GRNs show high similarity to the GRNs that operate in the cells that generate the cartilage-like tissues of basal chordate and invertebrates that do not produce mineralized tissue. These comparisons suggest that biomineralization in deuterostomes evolved through the phylum specific co-option of GRNs that control distinct organic scaffolds to mineralization.

Review: Post-translational modifications of marine shell matrix proteins

Shell matrix proteins (SMPs) are key components for the Mollusk shell biomineralization. SMPs function has been hypothesized in several proteins by bioinformatics analysis, and through in vitro crystallization assays. However, studies of the post-translational modifications (PTMs) of SMPs, which contribute to their structure and the function, are limited. This review provides the current status of the SMPs with the most common PTMs described (glycosylation, phosphorylation, and disulfide bond formation) and their role in shell biomineralization. Also, recent studies based on recombinant production of SMPs are discussed. Finally, recommendations for the study of SMPs and their PTMs are provided. The review showed that PTMs are widely distributed in SMPs, and their presence on SMPs may contribute to the modulation of their activity in some SMPs, contributing to the crystal growth formation and differentiation through different mechanisms, however, in a few cases the lack of the PTMs do not alter their inherent function.

On Biomineralization: Enzymes Switch on Mesocrystal Assembly

Cellular machineries guide the bottom-up pathways toward crystal superstructures based on the transport of inorganic precursors and their precise integration with organic frameworks. The biosynthesis of mesocrystalline spines entails concerted interactions between biomolecules and inorganic precursors; however, the bioinorganic interactions and interfaces that regulate material form and growth as well as the selective emergence of structural complexity in the form of nanostructured crystals are not clear. By investigating mineral nucleation under the regulation of recombinant proteins, we show that SpSM50, a matrix protein of the sea urchin spine, stabilizes mineral precursors via vesicle-confinement, a function conferred by a low-complexity, disordered region. Site-specific proteolysis of this domain by a collagenase initiates phase transformation of the confined mineral phase. The residual C-type lectin domain molds the fluidic mineral precursor into hierarchical mesocrystals identical to structural crystal modules constituting the biogenic mineral. Thus, the regulatory functions of proteolytic enzymes can guide biomacromolecular domain constitutions and interfaces, in turn determining inorganic phase transformations toward hybrid materials as well as integrating organic and inorganic components across hierarchical length scales. Bearing striking resemblance to biogenic mineralization, these hybrid materials recruit bioinorganic interactions which elegantly intertwine nucleation and crystallization phenomena with biomolecular structural dynamics, hence elucidating a long-sought key of how nature can orchestrate complex biomineralization processes.

Secrets of the Sea Urchin Spicule Revealed: Protein Cooperativity Is Responsible for ACC Transformation, Intracrystalline Incorporation, and Guided Mineral Particle Assembly in Biocomposite Material Formation

The formation of the sea urchin spicule involves the stabilization and transformation of amorphous calcium carbonate (ACC) and assembly of ACC nanoparticle precursors into a mesoscale single crystal of fracture-resistant calcite. This process of particle assembly or attachment is under the control of a family of proteins known as the spicule matrix [Strongylocentrotus purpuratus (SpSM)] proteome. Recently, two members of this proteome, SpSM50 and the glycoprotein SpSM30B/C-G (in recombinant forms), were found to interact together via SpSM30B/C-G oligosaccharide-SpSM50 protein interactions to form hybrid protein hydrogels with unique physical properties. In this study, we investigate the mineralization properties of this hybrid hydrogel alongside the hydrogels formed by SpSM50 and SpSM30B/C-G individually. We find that the SpSM50 + SpSM30B/C-G hybrid hydrogel is synergistic with regard to surface modifications and intracrystalline inclusions of existing calcite crystals, the inhibition of ACC formation, and the kinetic destabilization of ACC to form a crystalline phase. Most importantly, the hybrid hydrogel phase assembles and organizes mineral particles into discrete clusters or domains within in vitro mineralization environments. Thus, the interactions of SpSM50 and SpSM30B/C-G, mediated by carbohydrate-protein binding, reflect the need for protein cooperativity for the ACC-to-crystalline transformation, intracrystalline void formation, and guided mineral particle assembly processes that are instrumental in spicule formation.

Endocytosis in primary mesenchyme cells during sea urchin larval skeletogenesis

The sea urchin larval embryo elaborates two calcitic endoskeletal elements called spicules. Spicules are synthesized by the primary mesenchyme cells (PMCs) and begin to form at early gastrula stage. It is known that the calcium comprising the spicules comes from the seawater and we wish to further consider the mode of calcium transport from the extracellular seawater to the PMCs and then onto the forming spicules. We used PMC in vitro cultures, calcein, fluorescently labeled dextran, and fluorescently labeled Wheat Germ Agglutinin (WGA) to track calcium transport from the seawater into PMCs and spicules and to determine how molecules from the surface of PMCs interact with the incoming calcium. Labeling of PMC endocytic vesicles and forming spicules by both calcein and fluorescently tagged dextran indicate that calcium is taken up from the seawater by endocytosis and directly incorporated into spicules. Calcein labeling studies also indicate that calcium from the extracellular seawater begins to be incorporated into spicules within 30min of uptake. In addition, we demonstrate that fluorescently labeled WGA and calcein are taken up by many of the same endocytic vesicles and are incorporated into growing spicules. These findings suggest that PMC specific surface molecules accompany calcium ions as they enter PMCs via endocytosis and are incorporated together in the growing spicule. Using anti-spicule matrix protein antibodies, we pinpoint a subset of spicule matrix proteins that may accompany calcium ions from the surface of the PMCs until they are incorporated into spicules. Msp130 is identified as one of these spicule matrix proteins.

Temporal and spatial expression patterns of biomineralization proteins during early development in the stony coral Pocillopora damicornis

Reef-building corals begin as non-calcifying larvae that, upon settling, rapidly begin to accrete skeleton and a protein-rich skeletal organic matrix that attach them to the reef. Here, we characterized the temporal and spatial expression pattern of a suite of biomineralization genes during three stages of larval development in the reef-building coral Pocillopora damicornis: stage I, newly released; stage II, oral-aborally compressed and stage III, settled and calcifying spat. Transcriptome analysis revealed 3882 differentially expressed genes that clustered into four distinctly different patterns of expression change across the three developmental stages. Immunolocalization analysis further reveals the spatial arrangement of coral acid-rich proteins (CARPs) in the overall architecture of the emerging skeleton. These results provide the first analysis of the timing of the biomineralization 'toolkit' in the early life history of a stony coral.

A Model Sea Urchin Spicule Matrix Protein Self-Associates To Form Mineral-Modifying Protein Hydrogels

In the purple sea urchin Strongylocentrotus purpuratus, the formation and mineralization of fracture-resistant skeletal elements such as the embryonic spicule require the combinatorial participation of numerous spicule matrix proteins such as the SpSM30A-F isoforms. However, because of limited abundance, it has been difficult to pursue extensive biochemical studies of the SpSM30 proteins and deduce their role in spicule formation and mineralization. To circumvent these problems, we expressed a model recombinant spicule matrix protein, rSpSM30B/C, which possesses the key sequence attributes of isoforms "B" and "C". Our findings indicate that rSpSM30B/C is expressed in insect cells as a single polypeptide containing variations in glycosylation that create microheterogeneity in rSpSM30B/C molecular masses. These post-translational modifications incorporate O- and N-glycans and anionic mono- and bisialylated and mono- and bisulfated monosaccharides on the protein molecules and enhance its aggregation propensity. Bioinformatics and biophysical experiments confirm that rSpSM30B/C is an intrinsically disordered, aggregation-prone protein that forms porous protein hydrogels that control the in vitro mineralization process in three ways: (1) increase the time interval for prenucleation cluster formation and transiently stabilize an ACC polymorph, (2) promote and organize single-crystal calcite nanoparticles, and (3) promote faceted growth and create surface texturing of calcite crystals. These features are also common to mollusk shell nacre proteins, and we conclude that rSpSM30B/C is a spiculogenesis protein that exhibits traits found in other calcium carbonate mineral modification proteins.

Comparative Developmental Transcriptomics Reveals Rewiring of a Highly Conserved Gene Regulatory Network during a Major Life History Switch in the Sea Urchin Genus Heliocidaris

The ecologically significant shift in developmental strategy from planktotrophic (feeding) to lecithotrophic (nonfeeding) development in the sea urchin genus Heliocidaris is one of the most comprehensively studied life history transitions in any animal. Although the evolution of lecithotrophy involved substantial changes to larval development and morphology, it is not known to what extent changes in gene expression underlie the developmental differences between species, nor do we understand how these changes evolved within the context of the well-defined gene regulatory network (GRN) underlying sea urchin development. To address these questions, we used RNA-seq to measure expression dynamics across development in three species: the lecithotroph Heliocidaris erythrogramma, the closely related planktotroph H. tuberculata, and an outgroup planktotroph Lytechinus variegatus. Using well-established statistical methods, we developed a novel framework for identifying, quantifying, and polarizing evolutionary changes in gene expression profiles across the transcriptome and within the GRN. We found that major changes in gene expression profiles were more numerous during the evolution of lecithotrophy than during the persistence of planktotrophy, and that genes with derived expression profiles in the lecithotroph displayed specific characteristics as a group that are consistent with the dramatically altered developmental program in this species. Compared to the transcriptome, changes in gene expression profiles within the GRN were even more pronounced in the lecithotroph. We found evidence for conservation and likely divergence of particular GRN regulatory interactions in the lecithotroph, as well as significant changes in the expression of genes with known roles in larval skeletogenesis. We further use coexpression analysis to identify genes of unknown function that may contribute to both conserved and derived developmental traits between species. Collectively, our results indicate that distinct evolutionary processes operate on gene expression during periods of life history conservation and periods of life history divergence, and that this contrast is even more pronounced within the GRN than across the transcriptome as a whole.

Quantitative proteomics provides new insights into chicken eggshell matrix protein functions during the primary events of mineralisation and the active calcification phase

Eggshell is a bioceramic composed of 95% calcium carbonate mineral and 3.5% organic matrix. Its structural organisation is controlled by its organic matrix. We have used quantitative proteomics to study four key stages of shell mineralisation: 1) widespread deposition of amorphous calcium carbonate (ACC), 2) ACC transformation into crystalline calcite aggregates, 3) formation of larger calcite crystal units and 4) development of a columnar structure with preferential calcite crystal orientation. This approach explored the distribution of 216 shell matrix proteins found at the four stages. Variations in abundance according to these calcification events were observed for 175 proteins. A putative function related to the mineralisation process was predicted by bioinformatics for 77 of them and was further characterised. We confirmed the important role of lysozyme, ovotransferrin, ovocleidin-17 and ovocleidin-116 for shell calcification process, characterised major calcium binding proteins (EDIL3, ALB, MFGE8, NUCB2), and described novel proteoglycans core proteins (GPC4, HAPLN3). We suggest that OVAL and OC-17 play a role in the stabilisation of ACC. Finally, we report proteins involved in the regulation of proteins driving the mineralisation. They correspond to numerous molecular chaperones including CLU, PPIB and OCX21, protease and protease inhibitors including OVM and CST3, and regulators of phosphorylation.

SM50 repeat-polypeptides self-assemble into discrete matrix subunits and promote appositional calcium carbonate crystal growth during sea urchin tooth biomineralization

The two major proteins involved in vertebrate enamel formation and echinoderm sea urchin tooth biomineralization, amelogenin and SM50, are both characterized by elongated polyproline repeat domains in the center of the macromolecule. To determine the role of polyproline repeat polypeptides in basal deuterostome biomineralization, we have mapped the localization of SM50 as it relates to crystal growth, conducted self-assembly studies of SM50 repeat polypeptides, and examined their effect on calcium carbonate and apatite crystal growth. Electron micrographs of the growth zone of Strongylocentrotus purpuratus sea urchin teeth documented a series of successive events from intravesicular mineral nucleation to mineral deposition at the interface between tooth surface and odontoblast syncytium. Using immunohistochemistry, SM50 was detected within the cytoplasm of cells associated with the developing tooth mineral, at the mineral secreting front, and adjacent to initial mineral deposits, but not in muscles and ligaments. Polypeptides derived from the SM50 polyproline alternating hexa- and hepta-peptide repeat region (SM50P6P7) formed highly discrete, donut-shaped self-assembly patterns. In calcium carbonate crystal growth studies, SM50P6P7 repeat peptides triggered the growth of expansive networks of fused calcium carbonate crystals while in apatite growth studies, SM50P6P7 peptides facilitated the growth of needle-shaped and parallel arranged crystals resembling those found in developing vertebrate enamel. In comparison, SM50P6P7 surpassed the PXX24 polypeptide repeat region derived from the vertebrate enamel protein amelogenin in its ability to promote crystal nucleation and appositional crystal growth. Together, these studies establish the SM50P6P7 polyproline repeat region as a potent regulator in the protein-guided appositional crystal growth that occurs during continuous tooth mineralization and eruption. In addition, our studies highlight the role of species-specific polyproline repeat motifs in the formation of discrete self-assembled matrices and the resulting control of mineral growth.

Maternal Exposure to Cadmium and Manganese Impairs Reproduction and Progeny Fitness in the Sea Urchin Paracentrotus lividus

Metal contamination represents one of the major sources of pollution in marine environments. In this study we investigated the short-term effects of ecologically relevant cadmium and manganese concentrations (10(-6) and 3.6 x 10(-5) M, respectively) on females of the sea urchin Paracentrotus lividus and their progeny, reared in the absence or presence of the metal. Cadmium is a well-known heavy metal, whereas manganese represents a potential emerging contaminant, resulting from an increased production of manganese-containing compounds. The effects of these agents were examined on both P. lividus adults and their offspring following reproductive state, morphology of embryos, nitric oxide (NO) production and differential gene expression. Here, we demonstrated that both metals differentially impaired the fertilization processes of the treated female sea urchins, causing modifications in the reproductive state and also affecting NO production in the ovaries. A detailed analysis of the progeny showed a high percentage of abnormal embryos, associated to an increase in the endogenous NO levels and variations in the transcriptional expression of several genes involved in stress response, skeletogenesis, detoxification, multi drug efflux processes and NO production. Moreover, we found significant differences in the progeny from females exposed to metals and reared in metal-containing sea water compared to embryos reared in non-contaminated sea water. Overall, these results greatly expanded previous studies on the toxic effects of metals on P. lividus and provided new insights into the molecular events induced in the progeny of sea urchins exposed to metals.

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.

Investigating protein function in biomineralized tissues using molecular biology techniques

We describe modern molecular biology methods currently used in the study of biomineralization. We focus our descriptions on two areas of biomineralization research in which these methods have been particularly powerful. The first area is the use of modern molecular methods to identify and characterize the so-called occluded matrix proteins present in mineralized tissues. More specifically, we describe the use of RNA-seq and the next generation of DNA sequencers and the use of direct protein sequencing and mass spectrometers as ways of identifying proteins present in mineralized tissues. The second area is the use of molecular methods to examine the function of proteins in biomineralization. RNA interference (RNAi), morpholino antisense, and other methods are described and discussed as ways of elucidating protein function.

Lectin uptake and incorporation into the calcitic spicule of sea urchin embryos

Primary mesenchyme cells (PMCs) are skeletogenenic cells that produce a calcareous endoskeleton in developing sea urchin larvae. The PMCs fuse to form a cavity in which spicule matrix proteins and calcium are secreted forming the mineralized spicule. In this study, living sea urchin embryos were stained with fluorescently conjugated wheat germ agglutinin, a lectin that preferentially binds to PMCs, and the redistribution of this fluorescent tag was examined during sea urchin development. Initially, fluorescence was associated primarily with the surface of PMCs. Subsequently, the fluorescent label redistributed to intracellular vesicles in the PMCs. As the larval skeleton developed, intracellular granular staining diminished and fluorescence appeared in the spicules. Spicules that were cleaned to remove membranous material associated with the surface exhibited bright fluorescence, which indicated that fluorescently labelled lectin had been incorporated into the spicule matrix. The results provide evidence for a cellular pathway in which material is taken up at the cell surface, sequestered in intracellular vesicles and then incorporated into the developing spicule.

Crystallization and preliminary X-ray analysis of the C-type lectin domain of the spicule matrix protein SM50 from Strongylocentrotus purpuratus

Sea urchin spicules have a calcitic mesocrystalline architecture that is closely associated with a matrix of proteins and amorphous minerals. The mechanism underlying spicule formation involves complex processes encompassing spatio-temporally regulated organic-inorganic interactions. C-type lectin domains are present in several spicule matrix proteins in Strongylocentrotus purpuratus, implying their role in spiculogenesis. In this study, the C-type lectin domain of SM50 was overexpressed, purified and crystallized using a vapour-diffusion method. The crystal diffracted to a resolution of 2.85 Å and belonged to space group P212121, with unit-cell parameters a = 100.6, b = 115.4, c = 130.6 Å, α = β = γ = 90°. Assuming 50% solvent content, six chains are expected to be present in the asymmetric unit.

SM30 protein function during sea urchin larval spicule formation

A central issue in better understanding the process of biomineralization is to elucidate the function of occluded matrix proteins present in mineralized tissues. A potent approach to addressing this issue utilizes specific inhibitors of expression of known genes. Application of antisense oligonucleotides that specifically suppress translation of a given mRNA are capable of causing aberrant biomineralization, thereby revealing, at least in part, a likely function of the protein and gene under investigation. We have applied this approach to study the possible function(s) of the SM30 family of proteins, which are found in spicules, teeth, spines, and tests of Strongylocentrotus purpuratus as well as other euechinoid sea urchins. It is possible using the anti-SM30 morpholino-oligonucleotides (MO's) to reduce the level of these proteins to very low levels, yet the development of skeletal spicules in the embryo shows little or no aberration. This surprising result requires re-thinking about the role of these, and possibly other occluded matrix proteins.

Early developmental gene regulation in Strongylocentrotus purpuratus embryos in response to elevated CO₂ seawater conditions

Ocean acidification, or the increased uptake of CO(2) by the ocean due to elevated atmospheric CO(2) concentrations, may variably impact marine early life history stages, as they may be especially susceptible to changes in ocean chemistry. Investigating the regulatory mechanisms of early development in an environmental context, or ecological development, will contribute to increased understanding of potential organismal responses to such rapid, large-scale environmental changes. We examined transcript-level responses to elevated seawater CO(2) during gastrulation and the initiation of spiculogenesis, two crucial developmental processes in the purple sea urchin, Strongylocentrotus purpuratus. Embryos were reared at the current, accepted oceanic CO(2) concentration of 380 microatmospheres (μatm), and at the elevated levels of 1000 and 1350 μatm, simulating predictions for oceans and upwelling regions, respectively. The seven genes of interest comprised a subset of pathways in the primary mesenchyme cell gene regulatory network (PMC GRN) shown to be necessary for the regulation and execution of gastrulation and spiculogenesis. Of the seven genes, qPCR analysis indicated that elevated CO(2) concentrations only had a significant but subtle effect on two genes, one important for early embryo patterning, Wnt8, and the other an integral component in spiculogenesis and biomineralization, SM30b. Protein levels of another spicule matrix component, SM50, demonstrated significant variable responses to elevated CO(2). These data link the regulation of crucial early developmental processes with the environment that these embryos would be developing within, situating the study of organismal responses to ocean acidification in a developmental context.

The multiple effects of amino acids on the early stages of calcium carbonate crystallization

Proteins have found their way into many of Nature’s structures due to their structural stability, diversity in function and composition, and ability to be regulated as well as be regulators themselves. In this study, we investigate the constitutive amino acids that make up some of these proteins which are involved in CaCO3 mineralization – either in nucleation, crystal growth, or inhibition processes. By assaying all 20 amino acids with vapor diffusion and in situ potentiometric titration, we have found specific amino acids having multiple effects on the early stages of CaCO3 crystallization. These same amino acids have been independently implicated as constituents in liquid-like precursors that form mineralized tissues, processes believed to be key effects of biomineralization proteins in several biological model systems.

Transient precursor amorphous phases in biomineralization.In the footsteps of Heinz A. Lowenstam

Heinz A. Lowenstam’s discovery in 1967, together with Ken Towe that the magnetite mineral in mature chiton teeth forms from a disordered transient precursor phase, ferrihydrite, remained an isolated curiosity for 30 years. During the last 15 years, many more examples were found in both invertebrates and vertebrates, where the mature crystalline mineral phase is formed through a transient amorphous precursor phase. Here we review this widespread phenomenon, and also describe the details of the transformation process in the formation of the calcitic spicules of the sea urchin larva. We identify many open questions.

Biomineral ultrastructure, elemental constitution and genomic analysis of biomineralization-related proteins in hemichordates

Here, we report the discovery and characterization of biominerals in the acorn worms Saccoglossus bromophenolosus and Ptychodera flava galapagos (Phylum: Hemichordata). Using electron microscopy, X-ray microprobe analyses and confocal Raman spectroscopy, we show that hemichordate biominerals are small CaCO(3) aragonitic elements restricted to specialized epidermal structures, and in S. bromophenolosus, are apparently secreted by sclerocytes. Investigation of urchin biomineralizing proteins in the translated genome and expressed sequence tag (EST) libraries of Saccoglossus kowalevskii indicates that three members of the urchin MSP-130 family, a carbonic anhydrase and a matrix metaloprotease are present and transcribed during the development of S. kowalevskii. The SM family of proteins is absent from the hemichordate genome. These results increase the number of phyla known to biomineralize and suggest that some of the gene-regulatory 'toolkit', if not mineralized tissue themselves, may have been present in the common ancestor to hemichordates and echinoderms.

Phase transitions in biogenic amorphous calcium carbonate

Crystalline biominerals do not resemble faceted crystals. Current explanations for this property involve formation via amorphous phases. Using X-ray absorption near-edge structure (XANES) spectroscopy and photoelectron emission microscopy (PEEM), here we examine forming spicules in embryos of Strongylocentrotus purpuratus sea urchins, and observe a sequence of three mineral phases: hydrated amorphous calcium carbonate (ACC · H(2)O) → dehydrated amorphous calcium carbonate (ACC) → calcite. Unexpectedly, we find ACC · H(2)O-rich nanoparticles that persist after the surrounding mineral has dehydrated and crystallized. Protein matrix components occluded within the mineral must inhibit ACC · H(2)O dehydration. We devised an in vitro, also using XANES-PEEM, assay to identify spicule proteins that may play a role in stabilizing various mineral phases, and found that the most abundant occluded matrix protein in the sea urchin spicules, SM50, stabilizes ACC · H(2)O in vitro.

Structure-property relationships of a biological mesocrystal in the adult sea urchin spine

Structuring over many length scales is a design strategy widely used in Nature to create materials with unique functional properties. We here present a comprehensive analysis of an adult sea urchin spine, and in revealing a complex, hierarchical structure, show how Nature fabricates a material which diffracts as a single crystal of calcite and yet fractures as a glassy material. Each spine comprises a highly oriented array of Mg-calcite nanocrystals in which amorphous regions and macromolecules are embedded. It is postulated that this mesocrystalline structure forms via the crystallization of a dense array of amorphous calcium carbonate (ACC) precursor particles. A residual surface layer of ACC and/or macromolecules remains around the nanoparticle units which creates the mesocrystal structure and contributes to the conchoidal fracture behavior. Nature's demonstration of how crystallization of an amorphous precursor phase can create a crystalline material with remarkable properties therefore provides inspiration for a novel approach to the design and synthesis of synthetic composite materials.

Rapid adaptation to food availability by a dopamine-mediated morphogenetic response

Food can act as a powerful stimulus, eliciting metabolic, behavioural and developmental responses. These phenotypic changes can alter ecological and evolutionary processes; yet, the molecular mechanisms underlying many plastic phenotypic responses remain unknown. Here we show that dopamine signalling through a type-D(2) receptor mediates developmental plasticity by regulating arm length in pre-feeding sea urchin larvae in response to food availability. Although prey-induced traits are often thought to improve food acquisition, the mechanism underlying this plastic response acts to reduce feeding structure size and subsequent feeding rate. Consequently, the developmental programme and/or maternal provisioning predetermine the maximum possible feeding rate, and food-induced dopamine signalling reduces food acquisition potential during periods of abundant resources to preserve maternal energetic reserves. Sea urchin larvae may have co-opted the widespread use of food-induced dopamine signalling from behavioural responses to instead alter their development.

Biominerals--hierarchical nanocomposites: the example of bone

Many organisms incorporate inorganic solids in their tissues to enhance their functional, primarily mechanical, properties. These mineralized tissues, also called biominerals, are unique organo-mineral nanocomposites, organized at several hierarchical levels, from nano- to macroscale. Unlike man-made composite materials, which often are simple physical blends of their components, the organic and inorganic phases in biominerals interface at the molecular level. Although these tissues are made of relatively weak components under ambient conditions, their hierarchical structural organization and intimate interactions between different elements lead to superior mechanical properties. Understanding basic principles of formation, structure, and functional properties of these tissues might lead to novel bioinspired strategies for material design and better treatments for diseases of the mineralized tissues. This review focuses on general principles of structural organization, formation, and functional properties of biominerals on the example the bone tissues.

Molecular aspects of biomineralization of the echinoderm endoskeleton

Echinoderms possess a rigid endoskeleton composed of calcite and small amounts of occluded organic matrix proteins. The test (i.e., the shell-like structure of adults), spines, pedicellariae, tube feet, and teeth of adults, as well as delicate endoskeletal spicules found in larvae of some classes, are the main skeletal structures. They have been intensively studied for insight into the mechanisms of biomineralization. Recent work on characterization of the mineral phase and occluded proteins in embryonic skeletal spicules shows that these simple-looking structures contain scores of different proteins, and that the mineral phase is composed of amorphous calcium carbonate (ACC), which then transforms to an anhydrous ACC and eventually to calcite. Likewise, the adult tooth shows a similar transition from hydrated ACC to anhydrous ACC to calcite during its formation, and a similar transition is likely occurring during adult spine regeneration. We speculate that: (1) the ACC precursor is a general strategy employed in biomineralization in echinoderms, (2) the numerous occluded proteins play a role in post-secretion formation of the mature biomineralized structure, and (3) proteins with "multi-valent" intrinsically disordered domains are important for formation of occluded matrix structures, and regulation of crucial matrix-mineral interactions, such as ACC to calcite transitions and polymorph selection.

Proteomic analysis of sea urchin (Strongylocentrotus purpuratus) spicule matrix

BACKGROUND

The sea urchin embryo has been an important model organism in developmental biology for more than a century. This is due to its relatively simple construction, translucent appearance, and the possibility to follow the fate of individual cells as development to the pluteus larva proceeds. Because the larvae contain tiny calcitic skeletal elements, the spicules, they are also important model organisms for biomineralization research. Similar to other biominerals the spicule contains an organic matrix, which is thought to play an important role in its formation. However, only few spicule matrix proteins were identified previously.

RESULTS

Using mass spectrometry-based methods we have identified 231 proteins in the matrix of the S. purpuratus spicule matrix. Approximately two thirds of the identified proteins are either known or predicted to be extracellular proteins or transmembrane proteins with large ectodomains. The ectodomains may have been solubilized by partial proteolysis and subsequently integrated into the growing spicule. The most abundant protein of the spicule matrix is SM50. SM50-related proteins, SM30-related proteins, MSP130 and related proteins, matrix metalloproteases and carbonic anhydrase are among the most abundant components.

CONCLUSIONS

The spicule matrix is a relatively complex mixture of proteins not only containing matrix-specific proteins with a function in matrix assembly or mineralization, but also: 1) proteins possibly important for the formation of the continuous membrane delineating the mineralization space; 2) proteins for secretory processes delivering proteinaceous or non-proteinaceous precursors; 3) or proteins reflecting signaling events at the cell/matrix interface. Comparison of the proteomes of different skeletal matrices allows prediction of proteins of general importance for mineralization in sea urchins, such as SM50, SM30-E, SM29 or MSP130. The comparisons also help point out putative tissue-specific proteins, such as tooth phosphodontin or specific spicule matrix metalloproteases of the MMP18/19 group. Furthermore, the direct sequence analysis of peptides by MS/MS validates many predicted genes and confirms the existence of the corresponding proteins.

Transformation mechanism of amorphous calcium carbonate into calcite in the sea urchin larval spicule

Sea urchin larval spicules transform amorphous calcium carbonate (ACC) into calcite single crystals. The mechanism of transformation is enigmatic: the transforming spicule displays both amorphous and crystalline properties, with no defined crystallization front. Here, we use X-ray photoelectron emission spectromicroscopy with probing size of 40-200 nm. We resolve 3 distinct mineral phases: An initial short-lived, presumably hydrated ACC phase, followed by an intermediate transient form of ACC, and finally the biogenic crystalline calcite phase. The amorphous and crystalline phases are juxtaposed, often appearing in adjacent sites at a scale of tens of nanometers. We propose that the amorphous-crystal transformation propagates in a tortuous path through preexisting 40- to 100-nm amorphous units, via a secondary nucleation mechanism.

The sea urchin (Strongylocentrotus purpuratus) test and spine proteomes

BACKGROUND

The organic matrix of biominerals plays an important role in biomineral formation and in determining biomineral properties. However, most components of biomineral matrices remain unknown at present. In sea urchin, which is an important model organism for developmental biology and biomineralization, only few matrix components have been identified and characterized at the protein level. The recent publication of the Strongylocentrotus purpuratus genome sequence rendered possible not only the identification of possible matrix proteins at the gene level, but also the direct identification of proteins contained in matrices of skeletal elements by in-depth, high-accuracy, proteomic analysis.

RESULTS

We identified 110 proteins as components of sea urchin test and spine organic matrix. Fourty of these proteins occurred in both compartments while others were unique to their respective compartment. More than 95% of the proteins were detected in sea urchin skeletal matrices for the first time. The most abundant protein in both matrices was the previously characterized spicule matrix protein SM50, but at least eight other members of this group, many of them only known as conceptual translation products previously, were identified by mass spectrometric sequence analysis of peptides derived from in vitro matrix degradation. The matrices also contained proteins implicated in biomineralization processes previously by inhibition studies using antibodies or specific enzyme inhibitors, such as matrix metalloproteases and members of the mesenchyme-specific MSP130 family. Other components were carbonic anhydrase, collagens, echinonectin, a alpha2-macroglobulin-like protein and several proteins containing scavenger receptor cysteine-rich domains. A few possible signal transduction pathway components, such as GTP-binding proteins, a semaphorin and a possible tyrosine kinase were also identified.

CONCLUSION

This report presents the most comprehensive list of sea urchin skeletal matrix proteins available at present. The complex mixture of proteins identified in matrices of the sea urchin skeleton may reflect many different aspects of the mineralization process. Because LC-MS/MS-based methods directly measures peptides our results validate many predicted genes and confirm the existence of the corresponding proteins. Considering the many newly identified matrix proteins, this proteomic study may serve as a road map for the further exploration of biomineralization processes in an important model organism.

The dynamics of secretion during sea urchin embryonic skeleton formation

Skeleton formation involves secretion of massive amounts of mineral precursor, usually a calcium salt, and matrix proteins, many of which are deposited on, or even occluded within, the mineral. The cell biological underpinnings of this secretion and subsequent assembly of the biomineralized skeletal element is not well understood. We ask here what is the relationship of the trafficking and secretion of the mineral and matrix within the primary mesenchyme cells of the sea urchin embryo, cells that deposit the endoskeletal spicule. Fluorescent labeling of intracellular calcium deposits show mineral precursors are present in granules visible by light microscopy, from whence they are deposited in the endoskeletal spicule, especially at its tip. In contrast, two different matrix proteins tagged with GFP are present in smaller post-Golgi vesicles only seen by electron microscopy, and the secreted protein are only incorporated into the spicule in the vicinity of the cell of origin. The matrix protein, SpSM30B, is post-translationally modified during secretion, and this processing continues after its incorporation into the spicule. Our findings also indicate that the mineral precursor and two well characterized matrix proteins are trafficked by different cellular routes.

Evolutionary analysis of the cis-regulatory region of the spicule matrix gene SM50 in strongylocentrotid sea urchins

An evolutionary analysis of transcriptional regulation is essential to understanding the molecular basis of phenotypic diversity. The sea urchin is an ideal system in which to explore the functional consequence of variation in cis-regulatory sequences. We are particularly interested in the evolution of genes involved in the patterning and synthesis of its larval skeleton. This study focuses on the cis-regulatory region of SM50, which has already been characterized to a considerable extent in the purple sea urchin, Strongylocentrotus purpuratus. We have isolated the cis-regulatory region from 15 individuals of S. purpuratus as well as seven closely related species in the family Strongylocentrotidae. We have performed a variety of statistical tests and present evidence that the cis-regulatory elements upstream of the SM50 gene have been subject to positive selection along the lineage leading to S. purpuratus. In addition, we have performed electrophoretic mobility shift assays (EMSAs) and demonstrate that nucleotide substitutions within Element C affect the ability of nuclear proteins to bind to this cis-regulatory element among members of the family Strongylocentrotidae. We speculate that such changes in SM50 and other genes could accumulate to produce altered patterns of gene expression with functional consequences during skeleton formation.

Development and evolution of chordate cartilage

Deuterostomes are a monophyletic group of animals containing vertebrates, lancelets, tunicates, hemichordates, echinoderms, and xenoturbellids. Four out of these six extant groups-vertebrates, lancelets, tunicates, and hemichordates-have pharyngeal gill slits. All groups of deuterostome animals that have pharyngeal gill slits also have a pharyngeal skeleton supporting the pharyngeal openings, except tunicates. We previously found that pharyngeal cartilage in hemichordates and cephalochordates contains a fibrillar collagen protein similar to vertebrate type II collagen, but unlike vertebrate cartilage, the invertebrate deuterostome cartilages are acellular. We found SoxE and fibrillar collagen expression in the pharyngeal endodermal cells adjacent to where the cartilages form. These same endodermal epithelial cells also express Pax1/9, a marker of pharyngeal endoderm in vertebrates, lancelets, tunicates, and hemichordates. In situ experiments with a cephalochordate fibrillar collagen also showed expression in pharyngeal endoderm, as well as the ectoderm and the mesodermal coelomic pouches lining the gill bars. These results indicate that the pharyngeal endodermal cells are responsible for secretion of the cartilage in hemichordates, whereas in lancelets, all the pharyngeal cells surrounding the gill bars, ectodermal, endodermal, and mesodermal may be responsible for cartilage formation. We propose that endoderm secretion was primarily the ancestral mode of making pharyngeal cartilages in deuterostomes. Later the evolutionary origin of neural crest allowed co-option of the gene network for the secretion of pharyngeal cartilage matrix in the new migratory neural crest cell populations found in vertebrates.

Molluscan shell proteins: primary structure, origin, and evolution

In the last few years, the field of molluscan biomineralization has known a tremendous mutation, regarding fundamental concepts on biomineralization regulation as well as regarding the methods of investigation. The most recent advances deal more particularly with the structure of shell biominerals at nanoscale and the identification of an increasing number of shell matrix protein components. Although the matrix is quantitatively a minor constituent in the shell of mollusks (less than 5% w/w), it is, however, the major component that controls different aspects of the shell formation processes: synthesis of transient amorphous minerals and evolution to crystalline phases, choice of the calcium carbonate polymorph (calcite vs aragonite), organization of crystallites in complex shell textures (microstructures). Until recently, the classical paradigm in molluscan shell biomineralization was to consider that the control of shell synthesis was performed primarily by two antagonistic mechanisms: crystal nucleation and growth inhibition. New concepts and emerging models try now to translate a more complex reality, which is remarkably illustrated by the wide variety of shell proteins, characterized since the mid-1990s, and described in this chapter. These proteins cover a broad spectrum of pI, from very acidic to very basic. The primary structure of a number of them is composed of different modules, suggesting that these proteins are multifunctional. Some of them exhibit enzymatic activities. Others may be involved in cell signaling. The oldness of shell proteins is discussed, in relation with the Cambrian appearance of the mollusks as a mineralizing phylum and with the Phanerozoic evolution of this group. Nowadays, the extracellular calcifying shell matrix appears as a whole integrated system, which regulates protein-mineral and protein-protein interactions as well as feedback interactions between the biominerals and the calcifying epithelium that synthesized them. Consequently, the molluscan shell matrix may be a source of bioactive molecules that would offer interesting perspectives in biomaterials and biomedical fields.

Study of larval and adult skeletogenic cells in developing sea urchin larvae

The larval skeleton of sea urchin embryos is formed by primary mesenchyme cells (PMCs). Thereafter, the larvae start feeding and additional arms develop. An adult rudiment that contains spines, tube feet, tests, and other parts of the adult body is formed in the eight-armed larva. The cellular mechanism of the later skeletogenesis and the lineage of the adult skeletogenic cells are not known. In this study, the morphogenesis of larval and adult skeletons during larval development of the sea urchin Hemicentrotus pulcherrimus was investigated by immunostaining cells with PMC-specific monoclonal antibodies, which are useful markers of skeletogenic cells. All spicules and the associated cells in the later larvae were stained with the antibodies. We could observe the initiation of skeletal morphogenesis at each developmental stage and visualize the cellular basis of skeleton formation in whole-mount embryos that possessed an intact morphology. There were some similarities between PMCs and the later skeletogenic cells. Both had a rounded shape with some filopodia, and the antigen expression started just before overt spicule formation. In the later-stage embryos, cells with filopodia and faint antigen expression were observed migrating in the blastocoel or aggregating in the presumptive location of new skeletogenesis.

A genome-wide analysis of biomineralization-related proteins in the sea urchin Strongylocentrotus purpuratus

Biomineralization, the biologically controlled formation of mineral deposits, is of widespread importance in biology, medicine, and engineering. Mineralized structures are found in most metazoan phyla and often have supportive, protective, or feeding functions. Among deuterostomes, only echinoderms and vertebrates produce extensive biomineralized structures. Although skeletons appeared independently in these two groups, ancestors of the vertebrates and echinoderms may have utilized similar components of a shared genetic "toolkit" to carry out biomineralization. The present study had two goals. First, we sought to expand our understanding of the proteins involved in biomineralization in the sea urchin, a powerful model system for analyzing the basic cellular and molecular mechanisms that underlie this process. Second, we sought to shed light on the possible evolutionary relationships between biomineralization in echinoderms and vertebrates. We used several computational methods to survey the genome of the purple sea urchin Strongylocentrotus purpuratus for gene products involved in biomineralization. Our analysis has greatly expanded the collection of biomineralization-related proteins. We have found that these proteins are often members of small families encoded by genes that are clustered in the genome. Most of the proteins are sea urchin-specific; that is, they have no apparent homologues in other invertebrate deuterostomes or vertebrates. Similarly, many of the vertebrate proteins that mediate mineral deposition do not have counterparts in the S. purpuratus genome. Our findings therefore reveal substantial differences in the primary sequences of proteins that mediate biomineral formation in echinoderms and vertebrates, possibly reflecting loose constraints on the primary structures of the proteins involved. On the other hand, certain cellular and molecular processes associated with earlier events in skeletogenesis appear similar in echinoderms and vertebrates, leaving open the possibility of deeper evolutionary relationships.

The C-type lectin-like domain superfamily

The superfamily of proteins containing C-type lectin-like domains (CTLDs) is a large group of extracellular Metazoan proteins with diverse functions. The CTLD structure has a characteristic double-loop ('loop-in-a-loop') stabilized by two highly conserved disulfide bridges located at the bases of the loops, as well as a set of conserved hydrophobic and polar interactions. The second loop, called the long loop region, is structurally and evolutionarily flexible, and is involved in Ca2+-dependent carbohydrate binding and interaction with other ligands. This loop is completely absent in a subset of CTLDs, which we refer to as compact CTLDs; these include the Link/PTR domain and bacterial CTLDs. CTLD-containing proteins (CTLDcps) were originally classified into seven groups based on their overall domain structure. Analyses of the superfamily representation in several completely sequenced genomes have added 10 new groups to the classification, and shown that it is applicable only to vertebrate CTLDcps; despite the abundance of CTLDcps in the invertebrate genomes studied, the domain architectures of these proteins do not match those of the vertebrate groups. Ca2+-dependent carbohydrate binding is the most common CTLD function in vertebrates, and apparently the ancestral one, as suggested by the many humoral defense CTLDcps characterized in insects and other invertebrates. However, many CTLDs have evolved to specifically recognize protein, lipid and inorganic ligands, including the vertebrate clade-specific snake venoms, and fish antifreeze and bird egg-shell proteins. Recent studies highlight the functional versatility of this protein superfamily and the CTLD scaffold, and suggest further interesting discoveries have yet to be made.

Transmission electron microscopy characterization of macromolecular domain cavities and microstructure of single-crystal calcite tooth plates of the sea urchin Lytechinus variegatus

The calcite plates and prisms in Lytechinus variegatus teeth form a complex biocomposite and employ a myriad of strengthening and toughening strategies. These crystal elements have macromolecule-containing internal cavities that may act to prevent cleavage. Transmission electron microscopy employing a small objective aperture was used to quantify several characteristics of these cavities. Cavity diameters ranged from 10 to 225 nm, the mean cavity diameter was between 50 and 60 nm, and cavities comprised approximately 20% of the volume of the crystal. Some cavities exhibited faceting and trace analysis identified these planes as being predominately of {1014} type. Through focus series of micrographs show the cavities were homogeneously distributed throughout the foil. The electron beam decomposed a substance within cavities and this suggests that these cavities are filled with a hydrated organic phase.

Developmental biology meets materials science: Morphogenesis of biomineralized structures

Biomineralization is the process by which metazoa form hard minerals for support, defense, and feeding. The minerals so formed, e.g., teeth, bones, shells, carapaces, and spicules, are of considerable interest to chemists and materials scientists. The cell biology underlying biomineralization is not well understood. The study of the formation of mineralized structures in developing organisms offers opportunities for understanding some intriguing aspects of cell and developmental biology. Five examples of biomineralization are presented: (1) the formation of siliceous spicules and frustules in sponges and diatoms, respectively; (2) the structure of skeletal spicules composed of amorphous calcium carbonate in some tunicates; (3) the secretion of the prism and nacre of some molluscan shells; (4) the development of skeletal spicules of sea urchin embryos; and (5) the formation of enamel of vertebrate teeth. Some speculations on the cellular and molecular mechanisms that support biomineralization, and their evolutionary origins, are discussed.

The localization of occluded matrix proteins in calcareous spicules of sea urchin larvae

The sea urchin embryo forms calcareous endoskeletal spicules composed of calcite and an occluded protein matrix. Though the latter is approximately 0.1% of of the mass, the composite has substantially altered material properties, e.g., conchoidal fracture planes and increased hardness. Experiments were conducted to examine the localization of matrix proteins occluded in the mineral by use of immunocytochemistry coupled with scanning electron microscopy (SEM). The isolated, unfixed spicules were etched under relatively gentle conditions and exposed to affinity purified antibodies made against two different matrix proteins, as well as an antibody to the entire constellation of matrix proteins. Immunogold tagged secondary antibody was used to observe antibody localization in the back scatter mode of SEM. All proteins examined were very widely distributed throughout the calcite, supporting a model of the structure in which a multiprotein assemblage is woven with fine texture around microcrystalline domains of calcite. Gentle etching revealed a laminar arrangement of calcite solubility, consistent with a stepwise deposition of matrix and mineral to increase girth of the spicule.

Depth-resolved structural imaging by third-harmonic generation microscopy

Third harmonic generation microscopy is shown to be a robust method for obtaining structural information on a variety of biological specimens. Its nature allows depth-resolved imaging of inhomogeneities with virtually no background from surrounding homogeneous media. With an appropriate illumination geometry, third harmonic generation microscopy is shown to be particularly suitable for imaging of biogenic crystals, enabling extraction of the crystal orientation.