Skeletal Matrix Proteins Research Articles

Whole-Genome Sequencing Highlights Conservative Genomic Strategies of a Stress-Tolerant, Long-Lived Scleractinian Coral, Porites australiensis Vaughan, 1918

Massive corals of the genus Porites, common, keystone reef builders in the Indo-Pacific Ocean, are distinguished by their relative stress tolerance and longevity. In order to identify genetic bases of these attributes, we sequenced the complete genome of a massive coral, Porites australiensis. We developed a genome assembly and gene models of comparable quality to those of other coral genomes. Proteome analysis identified 60 Porites skeletal matrix protein genes, all of which show significant similarities to genes from other corals and even to those from a sea anemone, which has no skeleton. Nonetheless, 30% of its skeletal matrix proteins were unique to Porites and were not present in the skeletons of other corals. Comparative genomic analyses showed that genes widely conserved among other organisms are selectively expanded in Porites. Specifically, comparisons of transcriptomic responses of P. australiensis and Acropora digitifera, a stress-sensitive coral, reveal significant differences in regard to genes that respond to increased water temperature, and some of the genes expanded exclusively in Porites may account for the different thermal tolerances of these corals. Taken together, widely shared genes may have given rise to unique biological characteristics of Porites, massive skeletons and stress tolerance.

Insights into the Evolution of Shells and Love Darts of Land Snails Revealed from Their Matrix Proteins.

Over the past decade, many skeletal matrix proteins that are possibly related to calcification have been reported in various calcifying animals. Molluscs are among the most diverse calcifying animals and some gastropods have adapted to terrestrial ecological niches. Although many shell matrix proteins (SMPs) have already been reported in molluscs, most reports have focused on marine molluscs, and the SMPs of terrestrial snails remain unclear. In addition, some terrestrial stylommatophoran snails have evolved an additional unique calcified character, called a “love dart,” used for mating behavior. We identified 54 SMPs in the terrestrial snail Euhadra quaesita, and found that they contain specific domains that are widely conserved in molluscan SMPs. However, our results also suggest that some of them possibly have evolved independently by domain shuffling, domain recruitment, or gene co-option. We then identified four dart matrix proteins, and found that two of them are the same proteins as those identified as SMPs. Our results suggest that some dart matrix proteins possibly have evolved by independent gene co-option from SMPs during dart evolution events. These results provide a new perspective on the evolution of SMPs and “love darts” in land snails.

An Overview of the Medical Applications of Marine Skeletal Matrix Proteins.

In recent years, the medicinal potential of marine organisms has attracted increasing attention. This is due to their immense diversity and adaptation to unique ecological niches that has led to vast physiological and biochemical diversification. Among these organisms, marine calcifiers are an abundant source of novel proteins and chemical entities that can be used for drug discovery. Studies of the skeletal organic matrix proteins of marine calcifiers have focused on biomedical applications such as the identification of growth inducing proteins that can be used for bone regeneration, for example, 2/4 bone morphogenic proteins (BMP). Although a few reports on the functions of proteins derived from marine calcifiers can be found in the literature, marine calcifiers themselves remain an untapped source of proteins for the development of innovative pharmaceuticals. Following an overview of the current knowledge of skeletal organic matrix proteins from marine calcifiers, this review will focus on various aspects of marine skeletal protein research including sources, biosynthesis, structures, and possible strategies for chemical or physical modification. Special attention will be given to potential medical applications and recent discoveries of skeletal proteins and polysaccharides with biologically appealing characteristics. In addition, I will introduce an effective protocol for sample preparation and protein purification that includes isolation technology for biopolymers (of both soluble and insoluble organic matrices) from coralline algae. These algae are a widespread but poorly studied group of shallow marine calcifiers that have great potential for marine drug discovery.

Potential use of carbonatogenic bacteria in monuments biorestoration

The sea urchin endoskeleton consists of a magnesium-rich biocalcite comprising a small amount of occluded organic macromolecules. This structure constitutes a key-model for understanding the mineral — organics interplay, and for conceiving in vitro bio-inspired materials with tailored properties. Here we employed a deep-clean technique to purify the occluded proteins from adult Paracentrotus lividus tests. We characterized them by 1- and 2D-electrophoreses, ELISA and immunoblotting, and using liquid chromatography coupled with Mass Spectrometry (nanoLC-MS/MS), we identified two metalloenzymes (carbonic anhydrase and MMP), a set of MSP130 family members, several C-type lectins (SM29, SM41, PM27) and cytoskeletal proteins. We demonstrate the effect of the protein extract on the crystals, with an in vitro crystallization assay. We suggest that this small set of biomineralization proteins may represent a ‘minimal molecular crystallization toolkit’.Biominerals often exhibit superior chemical properties, when compared to their inorganic counterparts. This is due pro parte to the proteins that are occluded in the mineral. However, the limited available studies on biomineralization have not yet succeeded in identifying a minimal set of proteins directly involved in the formation of the biomineral in vivo and sufficiently required for in vitro precipitation. Indeed, the high number of proteins identified by high-throughput screening in the recent years does not encourage the possibility of recreating or tailoring the mineral in vitro. Thus, the identification of biomineralization proteins involved in protein–mineral interactions is highly awaited. In the present study, we used the sea urchin, Paracentrotus lividus (P. lividus), to identify the native proteins directly taking part in protein–mineral interactions. We employed an improved deep-clean technique to extract and purify the native occluded skeletal matrix proteins from the test and identified them by the highly sensitive technique of nanoLC-MS/MS. We show that this minimal set of proteins has a shaping effect on the formation of biocalcite in vitro. This work gives insights on the biomineralization of the sea urchin, while it paves the way for the identification of biomineralization proteins in other biomineralizing systems. Understanding the ‘biologically controlled mineralization’ will facilitate the in vitro formation and tailoring of biominerals in mild conditions for applications in medicine and materials science.

A minimal molecular toolkit for mineral deposition? Biochemistry and proteomics of the test matrix of adult specimens of the sea urchin Paracentrotus lividus

The sea urchin endoskeleton consists of a magnesium-rich biocalcite comprising a small amount of occluded organic macromolecules. This structure constitutes a key-model for understanding the mineral — organics interplay, and for conceiving in vitro bio-inspired materials with tailored properties. Here we employed a deep-clean technique to purify the occluded proteins from adult Paracentrotus lividus tests. We characterized them by 1- and 2D-electrophoreses, ELISA and immunoblotting, and using liquid chromatography coupled with Mass Spectrometry (nanoLC-MS/MS), we identified two metalloenzymes (carbonic anhydrase and MMP), a set of MSP130 family members, several C-type lectins (SM29, SM41, PM27) and cytoskeletal proteins. We demonstrate the effect of the protein extract on the crystals, with an in vitro crystallization assay. We suggest that this small set of biomineralization proteins may represent a ‘minimal molecular crystallization toolkit’. SignificanceBiominerals often exhibit superior chemical properties, when compared to their inorganic counterparts. This is due pro parte to the proteins that are occluded in the mineral. However, the limited available studies on biomineralization have not yet succeeded in identifying a minimal set of proteins directly involved in the formation of the biomineral in vivo and sufficiently required for in vitro precipitation. Indeed, the high number of proteins identified by high-throughput screening in the recent years does not encourage the possibility of recreating or tailoring the mineral in vitro. Thus, the identification of biomineralization proteins involved in protein–mineral interactions is highly awaited. In the present study, we used the sea urchin, Paracentrotus lividus (P. lividus), to identify the native proteins directly taking part in protein–mineral interactions. We employed an improved deep-clean technique to extract and purify the native occluded skeletal matrix proteins from the test and identified them by the highly sensitive technique of nanoLC-MS/MS. We show that this minimal set of proteins has a shaping effect on the formation of biocalcite in vitro. This work gives insights on the biomineralization of the sea urchin, while it paves the way for the identification of biomineralization proteins in other biomineralizing systems. Understanding the ‘biologically controlled mineralization’ will facilitate the in vitro formation and tailoring of biominerals in mild conditions for applications in medicine and materials science.

Characterization of the Teeth Skeletal Matrix from <i>Arbacia lixula</i>

The teeth of sea urchins are highly complex composite structures, composed predominantly of high magnesium calcite, and of a minor heterogeneous assemblage of organic macromolecules that are occluded within the mineral. The organic matrix fulfils important functions in mineralization, in addition to giving the mineral phase peculiar mechanical properties, different from that of purely inorganic calcite. Nevertheless, the composition and function of individual components of the organic matrix still remains largely unknown. Up to now, the detailed protein repertoire of teeth from a single sea urchin species (Strongylocentrotus purpuratus, order Camarodonta) was investigated. In this study, we characterized for the first time the teeth skeletal matrix of another sea urchin, Arbacia lixula (order Arbacioida). The acetic acid soluble and acetic acid insoluble matrices, namely ASM and AIM respectively, were extracted and characterized with different biochemical methods including mono-dimensional SDS-PAGE, FT-IR spectroscopy, HPAE-PAD for monosaccharide analysis, and finally, proteomics. In spite of the paucity of peptide data, several of them displayed a high abundance of hydrophobic residues, i.e., alanine, glycine and valine, and of the apolar proline. We assert that the alanine- and proline-rich domains are important features of some of the matrix proteins associated to the teeth of sea urchins. None of the known skeletal matrix proteins from S. purpuratus teeth were identified in the organic matrix of A. lixula teeth. This might suggest major differences in teeth matrix protein repertoires of these two species belonging to orders that diverged in the Mesozoic times.

Immunolocalization of skeletal matrix proteins in tissue and mineral of the coral Stylophora pistillata.

The precipitation and assembly of calcium carbonate skeletons by stony corals is a precisely controlled process regulated by the secretion of an ECM. Recently, it has been reported that the proteome of the skeletal organic matrix (SOM) contains a group of coral acid-rich proteins as well as an assemblage of adhesion and structural proteins, which together, create a framework for the precipitation of aragonite. To date, we are aware of no report that has investigated the localization of individual SOM proteins in the skeleton. In particular, no data are available on the ultrastructural mapping of these proteins in the calcification site or the skeleton. This information is crucial to assessing the role of these proteins in biomineralization. Immunological techniques represent a valuable approach to localize a single component within a calcified skeleton. By using immunogold labeling and immunohistochemical assays, here we show the spatial arrangement of key matrix proteins in tissue and skeleton of the common zooxanthellate coral, Stylophora pistillata. To our knowledge, our results reveal for the first time that, at the nanoscale, skeletal proteins are embedded within the aragonite crystals in a highly ordered arrangement consistent with a diel calcification pattern. In the tissue, these proteins are not restricted to the calcifying epithelium, suggesting that they also play other roles in the coral's metabolic pathways.

The skeleton of the staghorn coral Acropora millepora: molecular and structural characterization.

The scleractinian coral Acropora millepora is one of the most studied species from the Great Barrier Reef. This species has been used to understand evolutionary, immune and developmental processes in cnidarians. It has also been subject of several ecological studies in order to elucidate reef responses to environmental changes such as temperature rise and ocean acidification (OA). In these contexts, several nucleic acid resources were made available. When combined to a recent proteomic analysis of the coral skeletal organic matrix (SOM), they enabled the identification of several skeletal matrix proteins, making A. millepora into an emerging model for biomineralization studies. Here we describe the skeletal microstructure of A. millepora skeleton, together with a functional and biochemical characterization of its occluded SOM that focuses on the protein and saccharidic moieties. The skeletal matrix proteins show a large range of isoelectric points, compositional patterns and signatures. Besides secreted proteins, there are a significant number of proteins with membrane attachment sites such as transmembrane domains and GPI anchors as well as proteins with integrin binding sites. These features show that the skeletal proteins must have strong adhesion properties in order to function in the calcifying space. Moreover this data suggest a molecular connection between the calcifying epithelium and the skeletal tissue during biocalcification. In terms of sugar moieties, the enrichment of the SOM in arabinose is striking, and the monosaccharide composition exhibits the same signature as that of mucus of acroporid corals. Finally, we observe that the interaction of the acetic acid soluble SOM on the morphology of in vitro grown CaCO3 crystals is very pronounced when compared with the calcifying matrices of some mollusks. In light of these results, we wish to commend Acropora millepora as a model for biocalcification studies in scleractinians, from molecular and structural viewpoints.

The sea urchin (Strongylocentrotus purpuratus) test and spine proteomes.

BackgroundThe 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.ResultsWe 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 α2-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.ConclusionThis 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.

Skeletal matrix proteins of invertebrate animals: Comparative analysis of their amino acid sequences

The genetic bases of skeletogenesis are expected to shed light on the origins of metazoan biomineralization. Here we review aspects of genetic machineries of invertebrate skeletogenesis, including regulatory genes involved in biomineralization as well, and with an enumerative reference to the genes encoding skeletal matrix proteins. The complete primary structure has been determined for a total of 77 skeletal matrix proteins in invertebrates representing five animal phyla. Presence of repeated sequences and prevalence of acidic proteins stand as common features among those proteins. Similarities are interpreted as convergence because these proteins are not similar at the primary structure level. C-type lectin-like domains are shared by the calcium carbonate skeletal matrix proteins of molluscs and deuterostomes. However, the important sites for carbohydrate binding are not conserved between these two groups. Several arthropod skeletal matrix proteins have the Rebers-Riddiford consensus sequence which is characteristic of non-calcified cuticular proteins of arthropods, indicating that these skeletal matrix proteins were recruited from the non-calcified cuticular proteins after arthropods diverged from other metazoan groups. Dermatopontin, a molluscan shell matrix protein, is also inferred to represent a cooption for biomineralization after molluscs diverged from other metazoan groups based on the molecular phylogemetic analysis. Those findings support the premise that the genetic machineries of biomineralization evolved independently many times after the divergence of metazoan phyla, and that some common genes that served for other functions have been coopted for biomineralization in various lineages.

Cartilage abnormalities are associated with abnormal Phex expression and with altered matrix protein and MMP-9 localization in Hyp mice

X-linked hypophosphatemic rickets (HYP) in humans is caused by mutations in the PHEX gene. This gene mutation is also found in Hyp mice, the murine homologue of the human disease. At present, it is unknown why loss of Phex function leads to cartilage abnormalities in Hyp mice. In the present study, we compared in wild-type and Hyp mice Phex protein localization in cartilage of developing long bone as well as localization of skeletal matrix proteins and matrix metalloproteinase-9 (MMP-9). Also compared were chondrocyte apoptosis in the growth plate, mineralization and cartilage remnant retention in the metaphysis, and chondroclast/osteoclast characteristics in the primary spongiosa. Phex protein was detected in proliferating and hypertrophic chondrocytes in growth plate cartilage of wild-type mice, but not in Hyp mice. Hyp mice exhibited a widened and irregular hypertrophic zone in growth plate cartilage showing hypomineralization, increased cartilage remnants from the growth plate in both metaphyseal trabecular and cortical bone, and fewer and smaller chondroclasts/osteoclasts in the primary spongiosa. Increased link protein and C-propeptide of type II procollagen of Hyp mice reflected the increase in chondrocytes and matrix in the cartilaginous growth plate and in bone. In addition, growth plate osteocalcin and bone sialoprotein levels were decreased, while osteonectin was increased, in hypertrophic chondrocytes and cartilage matrix in Hyp mice. MMP-9 in hypertrophic chondrocytes was also reduced in Hyp mice and fewer apoptotic hypertrophic chondrocytes were detected. These findings suggest that Phex may control mineralization and removal of hypertrophic chondrocytes and cartilage matrix in growth plate by regulating the synthesis and deposition of certain bone matrix proteins and proteases such as MMP-9.

SM37, a skeletogenic gene of the sea urchin embryo linked to the SM50 gene.

The genomic DNA region that contains the SM50 gene also included a second gene that appeared to encode another skeletogenic matrix protein. The two genes were linked at a distance of about 12 kb. Based on the molecular weight of the implied protein the gene was termed SM37. The SM37 protein included a long tandem sequence of short glycine-rich repeats that was similar to the glycine-rich repeats included in the SM50 protein and several other skeletal matrix proteins, although the sequence of SM37 repeat was distinct. The overall structure of the SM37 protein was similar to SM50 as well. However, SM37 was only about 30% identical in amino acid sequence to SM50, and coding region probes behaved as a single copy sequence under standard conditions. The SM37 gene included the same cis-regulatory elements as the SM50 gene, although in a different order with respect to transcription. This gene was regulated coordinately with SM50 during development, and like SM50 was expressed exclusively in skeletogenic mesenchyme lineages.

A regulatory domain that directs lineage-specific expression of a skeletal matrix protein gene in the sea urchin embryo.

DNA sequences derived from the 5' region of a gene coding for the 50-kD skeletal matrix protein (SM50) of sea urchin embryo spicules were linked to the CAT reporter gene and injected into unfertilized eggs. CAT mRNA and enzyme were synthesized from these fusion constructs in embryos derived from these eggs, and in situ hybridization with a CAT antisense RNA probe demonstrated that expression is confined to skeletogenic mesenchyme cells. A mean of 5.5 of the 32-blastula-stage skeletogenic mesenchyme cells displayed CAT mRNA (range 1-15), a result consistent with earlier measurements indicating that incorporation of the exogenous injected DNA probably occurs in a single blastomere during early cleavage. In vitro mutagenesis and deletion experiments showed that CAT enzyme activity in the transgenic embryos is enhanced 34-fold by decreasing the number of SM50 amino acids at the amino-terminus of the fusion protein from 43 to 4. cis-regulatory sequences that are sufficient to promote lineage-specific spatial expression in the embryo are located between -440 and +120 with respect to the transcriptional initiation site.

Aragonite in fossils

The distribution of aragonite in the skeletal parts of living organisms is reviewed, and its distribution in fossils is described on the basis of several hundred new determinations. Aragonitic fossils are extensively preserved in Tertiary sediments, and are common in Mesozoic rocks, particularly where the enclosing lithology is argillaceous. No aragonite was found by the authors in fossils from Palaeozoic rocks. The most important requirement for the preservation of aragonite is the presence of reducing conditions. It is suggested that the preservation of aragonite is due to the protective effect of organic skeletal matrix, which in turn requires reducing conditions for its preservation. The protective action of the organic matrix is attributed to the formation of a hydrophobic monomolecular layer on the crystal surface, composed of aminoacids derived from the breakdown of skeletal matrix proteins.