1
|
The Evolution of Biomineralization through the Co-Option of Organic Scaffold Forming Networks. Cells 2022; 11:cells11040595. [PMID: 35203246 PMCID: PMC8870065 DOI: 10.3390/cells11040595] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 12/05/2022] Open
Abstract
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.
Collapse
|
2
|
Rivera-Pérez C, Hernández-Saavedra NY. Review: Post-translational modifications of marine shell matrix proteins. Comp Biochem Physiol B Biochem Mol Biol 2021; 256:110641. [PMID: 34182126 DOI: 10.1016/j.cbpb.2021.110641] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/13/2021] [Accepted: 06/22/2021] [Indexed: 11/18/2022]
Abstract
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.
Collapse
Affiliation(s)
- Crisalejandra Rivera-Pérez
- CONACYT, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, Mexico.
| | - Norma Y Hernández-Saavedra
- Molecular Genetics Laboratory, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz 23096, Baja California Sur, Mexico
| |
Collapse
|
3
|
Takeuchi T, Fujie M, Koyanagi R, Plasseraud L, Ziegler-Devin I, Brosse N, Broussard C, Satoh N, Marin F. The 'Shellome' of the Crocus Clam Tridacna crocea Emphasizes Essential Components of Mollusk Shell Biomineralization. Front Genet 2021; 12:674539. [PMID: 34168677 PMCID: PMC8217771 DOI: 10.3389/fgene.2021.674539] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/13/2021] [Indexed: 01/31/2023] Open
Abstract
Molluscan shells are among the most fascinating research objects because of their diverse morphologies and textures. The formation of these delicate biomineralized structures is a matrix-mediated process. A question that arises is what are the essential components required to build these exoskeletons. In order to understand the molecular mechanisms of molluscan shell formation, it is crucial to identify organic macromolecules in different shells from diverse taxa. In the case of bivalves, however, taxon sampling in previous shell proteomics studies are focused predominantly on representatives of the class Pteriomorphia such as pearl oysters, edible oysters and mussels. In this study, we have characterized the shell organic matrix from the crocus clam, Tridacna crocea, (Heterodonta) using various biochemical techniques, including SDS-PAGE, FT-IR, monosaccharide analysis, and enzyme-linked lectin assay (ELLA). Furthermore, we have identified a number of shell matrix proteins (SMPs) using a comprehensive proteomics approach combined to RNA-seq. The biochemical studies confirmed the presence of proteins, polysaccharides, and sulfates in the T. crocea shell organic matrix. Proteomics analysis revealed that the majority of the T. crocea SMPs are novel and dissimilar to known SMPs identified from the other bivalve species. Meanwhile, the SMP repertoire of the crocus clam also includes proteins with conserved functional domains such as chitin-binding domain, VWA domain, and protease inhibitor domain. We also identified BMSP (Blue Mussel Shell Protein, originally reported from Mytilus), which is widely distributed among molluscan shell matrix proteins. Tridacna SMPs also include low-complexity regions (LCRs) that are absent in the other molluscan genomes, indicating that these genes may have evolved in specific lineage. These results highlight the diversity of the organic molecules – in particular proteins – that are essential for molluscan shell formation.
Collapse
Affiliation(s)
- Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Manabu Fujie
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Ryo Koyanagi
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Laurent Plasseraud
- Institut de Chimie Moléculaire de l'Université de Bourgogne, UMR CNRS 6302, Faculté des Sciences Mirande, Université de Bourgogne - Franche-Comté (UBFC), Dijon, France
| | - Isabelle Ziegler-Devin
- LERMAB, Faculté des Sciences et Technologies - Campus Aiguillettes, Université de Lorraine, Vandoeuvre-Lès-Nancy, France
| | - Nicolas Brosse
- LERMAB, Faculté des Sciences et Technologies - Campus Aiguillettes, Université de Lorraine, Vandoeuvre-Lès-Nancy, France
| | - Cédric Broussard
- 3P5 Proteomic Platform, Cochin Institute, University of Paris, INSERM U1016, CNRS UMR 8104, Paris, France
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Frédéric Marin
- UMR CNRS 6282 Biogéosciences, Bâtiment des Sciences Gabriel, Université de Bourgogne - Franche-Comté (UBFC), Dijon, France
| |
Collapse
|
4
|
Morgulis M, Winter MR, Shternhell L, Gildor T, Ben-Tabou de-Leon S. VEGF signaling activates the matrix metalloproteinases, MmpL7 and MmpL5 at the sites of active skeletal growth and MmpL7 regulates skeletal elongation. Dev Biol 2021; 473:80-89. [PMID: 33577829 DOI: 10.1016/j.ydbio.2021.01.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 12/20/2022]
Abstract
Organisms can uptake minerals, shape them in different forms and generate teeth, skeletons or shells that support and protect them. Mineral uptake, trafficking and nucleation are tightly regulated by the biomineralizing cells through networks of specialized proteins. Specifically, matrix metalloproteases (MMPs) digest various extracellular substrates and allow for mineralization in the vertebrates' teeth and bones, but little is known about their role in invertebrates' systems. The sea urchin embryo provides an excellent invertebrate model for genetic and molecular studies of biomineralization. MMP inhibition prevents the growth of the calcite spicules of the sea urchin larval skeleton, however, the molecular mechanisms and genes that underlie this response are not well understood. Here we study the spatial expression and regulation of two membrane type MMPs that were found to be occluded in the sea urchin spicules, Pl-MmpL7 and Pl-MmpL5, and investigate the function of Pl-MmpL7 in skeletogenesis. The inhibition of MMPs does not change the volume of the calcium vesicles in the skeletogenic cells. The expression of Pl-MmpL7 and Pl-MmpL5 is regulated by the Vascular Endothelial Growth Factor (VEGF) signaling, from the time of skeleton initiation and on. The expression of these genes is localized to the subsets of skeletogenic cells where active spicule growth occurs throughout skeletogenesis. Downregulation of Pl-MmpL7 expression delays the growth of the skeletal rods and in some cases, strongly perturbs skeletal shape. The localized expression of Pl-MmpL7 and Pl-MmpL5 to the active growth zone and the effect of Pl-MmpL7 perturbations on skeletal growth, suggest that these genes are essential for normal spicule elongation in the sea urchin embryo.
Collapse
Affiliation(s)
- Miri Morgulis
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 31905, Israel
| | - Mark R Winter
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 31905, Israel
| | - Ligal Shternhell
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 31905, Israel
| | - Tsvia Gildor
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 31905, Israel
| | - Smadar Ben-Tabou de-Leon
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 31905, Israel.
| |
Collapse
|
5
|
Abstract
Much recent marine research has been directed towards understanding the effects of anthropogenic-induced environmental change on marine biodiversity, particularly for those animals with heavily calcified exoskeletons, such as corals, molluscs and urchins. This is because life in our oceans is becoming more challenging for these animals with changes in temperature, pH and salinity. In the future, it will be more energetically expensive to make marine skeletons and the increasingly corrosive conditions in seawater are expected to result in the dissolution of these external skeletons. However, initial predictions of wide-scale sensitivity are changing as we understand more about the mechanisms underpinning skeletal production (biomineralization). These studies demonstrate the complexity of calcification pathways and the cellular responses of animals to these altered conditions. Factors including parental conditioning, phenotypic plasticity and epigenetics can significantly impact the production of skeletons and thus future population success. This understanding is paralleled by an increase in our knowledge of the genes and proteins involved in biomineralization, particularly in some phyla, such as urchins, molluscs and corals. This Review will provide a broad overview of our current understanding of the factors affecting skeletal production in marine invertebrates. It will focus on the molecular mechanisms underpinning biomineralization and how knowledge of these processes affects experimental design and our ability to predict responses to climate change. Understanding marine biomineralization has many tangible benefits in our changing world, including improvements in conservation and aquaculture and exploitation of natural calcified structure design using biomimicry approaches that are aimed at producing novel biocomposites.
Collapse
Affiliation(s)
- Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| |
Collapse
|
6
|
Organic matrices in metazoan calcium carbonate skeletons: Composition, functions, evolution. J Struct Biol 2016; 196:98-106. [DOI: 10.1016/j.jsb.2016.04.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/04/2016] [Accepted: 04/12/2016] [Indexed: 11/23/2022]
|
7
|
Katow H. Mechanisms of the epithelial-to-mesenchymal transition in sea urchin embryos. Tissue Barriers 2015; 3:e1059004. [PMID: 26716069 PMCID: PMC4681286 DOI: 10.1080/21688370.2015.1059004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 05/25/2015] [Accepted: 05/29/2015] [Indexed: 12/30/2022] Open
Abstract
Sea urchin mesenchyme is composed of the large micromere-derived spiculogenetic primary mesenchyme cells (PMC), veg2-tier macromere-derived non-spiculogenetic mesenchyme cells, the small micromere-derived germ cells, and the macro- and mesomere-derived neuronal mesenchyme cells. They are formed through the epithelial-to-mesenchymal transition (EMT) and possess multipotency, except PMCs that solely differentiate larval spicules. The process of EMT is associated with modification of epithelial cell surface property that includes loss of affinity to the apical and basal extracellular matrices, inter-epithelial cell adherens junctions and epithelial cell surface-specific proteins. These cell surface structures and molecules are endocytosed during EMT and utilized as initiators of cytoplasmic signaling pathways that often initiate protein phosphorylation to activate the gene regulatory networks. Acquisition of cell motility after EMT in these mesenchyme cells is associated with the expression of proteins such as Lefty, Snail and Seawi. Structural simplicity and genomic database of this model will further promote detailed EMT research.
Collapse
Affiliation(s)
- Hideki Katow
- Research Center for Marine Biology; Tohoku University; Asamushi, Aomori, Japan
| |
Collapse
|
8
|
Echinoderms: Hierarchically Organized Light Weight Skeletons. BIOLOGICALLY-INSPIRED SYSTEMS 2015. [DOI: 10.1007/978-94-017-9398-8_8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
9
|
Le Roy N, Jackson DJ, Marie B, Ramos-Silva P, Marin F. The evolution of metazoan α-carbonic anhydrases and their roles in calcium carbonate biomineralization. Front Zool 2014. [DOI: 10.1186/s12983-014-0075-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
|
10
|
Nam AS, Yin Y, von Marschall Z, Fisher LW. Efficient trafficking of acidic proteins out of the endoplasmic reticulum involves a conserved amino terminal IleProVal (IPV)-like tripeptide motif. Connect Tissue Res 2014; 55 Suppl 1:138-41. [PMID: 24844412 PMCID: PMC4153534 DOI: 10.3109/03008207.2014.923852] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Most of the proposed extracellular biomineralization processes include the secretion of proteins that interact with mineral ions and/or mineral surfaces. Typically these proteins are acidic or have acidic domains that interact with multivalent cations in the extracellular environment. We propose that most acidic, Ca(2+)-binding proteins challenge the cell's mechanisms for trafficking through the endoplasmic reticulum (ER) lumen due to lumenal mM calcium that cause them to form large aggregates. We have recently shown that >95% of the DSPP mutations that cause non-syndromic genetic dentin diseases start their dominant negative affects by failing to rapidly exit the ER likely by forming complexes that cannot be normally trafficked to the Golgi. The complexes of mutant DSPP then capture more (severe disease) or less (mild disease) of the DSPP translated from the normal allele. After searching genomic databases as well as the published literature, we found the IleProVal (IPV)-like motif at the predicted amino terminus of many acidic proteins made in the mineralizing as well as non-mineralizing tissues of many species including vertebrates, echinoderms, mollusks, and yeast. While we often focused on acidic proteins reported associated with mineralizing structures, proteins associated with hormones and their storage/secretion, digestion, blood functions, as well as milk and other secreted fluids started with variations of the motif. Our hypothesis is that the IPV-like motif interacts with a highly conserved cargo receptor in the ER that efficiently traffics the acidic proteins out of the organelle before they can form harmful aggregates in the Ca(2+)-rich lumen.
Collapse
Affiliation(s)
| | | | | | - Larry W. Fisher
- corresponding author: Room 223, Building 30, 9000 Rockville Pike, Bethesda, MD, 20892-4320. Phone: 301-496-5769, Fax: 301-402-0824,
| |
Collapse
|
11
|
Mann K, Edsinger E. The Lottia gigantea shell matrix proteome: re-analysis including MaxQuant iBAQ quantitation and phosphoproteome analysis. Proteome Sci 2014; 12:28. [PMID: 25018669 PMCID: PMC4094399 DOI: 10.1186/1477-5956-12-28] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 05/01/2014] [Indexed: 12/29/2022] Open
Abstract
Background Although the importance of proteins of the biomineral organic matrix and their posttranslational modifications for biomineralization is generally recognized, the number of published matrix proteomes is still small. This is mostly due to the lack of comprehensive sequence databases, usually derived from genomic sequencing projects. However, in-depth mass spectrometry-based proteomic analysis, which critically depends on high-quality sequence databases, is a very fast tool to identify candidates for functional biomineral matrix proteins and their posttranslational modifications. Identification of such candidate proteins is facilitated by at least approximate quantitation of the identified proteins, because the most abundant ones may also be the most interesting candidates for further functional analysis. Results Re-quantification of previously identified Lottia shell matrix proteins using the intensity-based absolute quantification (iBAQ) method as implemented in the MaxQuant identification and quantitation software showed that only 57 of the 382 accepted identifications constituted 98% of the total identified matrix proteome. This group of proteins did not contain obvious intracellular proteins, such as cytoskeletal components or ribosomal proteins, invariably identified as minor components of high-throughput biomineral matrix proteomes. Fourteen of these major proteins were phosphorylated to a variable extent. All together we identified 52 phospho sites in 20 of the 382 accepted proteins with high confidence. Conclusions We show that iBAQ quantitation may be a useful tool to narrow down the group of functional biomineral matrix protein candidates for further research in cell biology, genetics or materials research. Knowledge of posttranslational modifications in these major proteins could be a valuable addition to previously published proteomes. This is true especially for phosphorylation, because this modification was already shown to modify mineralization processes in some instances.
Collapse
Affiliation(s)
- Karlheinz Mann
- Max-Planck-Institut für Biochemie, Abteilung Proteomics und Signaltransduktion, Am Klopferspitz 18, Martinsried D-82152, Germany
| | - Eric Edsinger
- Rokhsar Department, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA ; Present address: Brenner Unit, Okinawa institute of Science and Technology, 1919-0 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| |
Collapse
|
12
|
Abstract
Biomineralization is the process by which living organisms deposit mineral in the extracellular matrix. In nature, almost 50% of biominerals are calcium-bearing minerals. In addition to calcium, we find biominerals formed from silica and magnetite. Calcium-containing biominerals could be either calcium phosphate as in apatite found in vertebrates or calcium carbonate as in calcite and aragonite found in many invertebrates. Since all biomineralization is matrix mediated, an understanding of the nature of the proteins involved is essential in elucidating its mechanism. This review will discuss some of the proteins involved in the process of biomineralization involving calcium. Two proteins, dentin matrix protein 1 and dentin phosphoprotein (Phosphophoryn) will serve as models for the vertebrate system, and two others - P16 and phosphodontin will serve as models for the invertebrate system.
Collapse
Affiliation(s)
- Keith Alvares
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL. 60611
| |
Collapse
|
13
|
Garfield DA, Runcie DE, Babbitt CC, Haygood R, Nielsen WJ, Wray GA. The impact of gene expression variation on the robustness and evolvability of a developmental gene regulatory network. PLoS Biol 2013; 11:e1001696. [PMID: 24204211 PMCID: PMC3812118 DOI: 10.1371/journal.pbio.1001696] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 09/16/2013] [Indexed: 11/18/2022] Open
Abstract
Regulatory interactions buffer development against genetic and environmental perturbations, but adaptation requires phenotypes to change. We investigated the relationship between robustness and evolvability within the gene regulatory network underlying development of the larval skeleton in the sea urchin Strongylocentrotus purpuratus. We find extensive variation in gene expression in this network throughout development in a natural population, some of which has a heritable genetic basis. Switch-like regulatory interactions predominate during early development, buffer expression variation, and may promote the accumulation of cryptic genetic variation affecting early stages. Regulatory interactions during later development are typically more sensitive (linear), allowing variation in expression to affect downstream target genes. Variation in skeletal morphology is associated primarily with expression variation of a few, primarily structural, genes at terminal positions within the network. These results indicate that the position and properties of gene interactions within a network can have important evolutionary consequences independent of their immediate regulatory role.
Collapse
Affiliation(s)
- David A. Garfield
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Daniel E. Runcie
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Courtney C. Babbitt
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
| | - Ralph Haygood
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- Center for Systems Biology, Duke University, Durham, North Carolina, United States of America
| | - William J. Nielsen
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
| | - Gregory A. Wray
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
- Center for Systems Biology, Duke University, Durham, North Carolina, United States of America
- * E-mail:
| |
Collapse
|
14
|
Mass T, Drake J, Haramaty L, Kim J, Zelzion E, Bhattacharya D, Falkowski P. Cloning and Characterization of Four Novel Coral Acid-Rich Proteins that Precipitate Carbonates In Vitro. Curr Biol 2013; 23:1126-31. [DOI: 10.1016/j.cub.2013.05.007] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 04/17/2013] [Accepted: 05/07/2013] [Indexed: 01/09/2023]
|
15
|
Rahman MA, Shinjo R, Oomori T, Wörheide G. Analysis of the proteinaceous components of the organic matrix of calcitic sclerites from the soft coral Sinularia sp. PLoS One 2013; 8:e58781. [PMID: 23527022 PMCID: PMC3597568 DOI: 10.1371/journal.pone.0058781] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 02/08/2013] [Indexed: 01/20/2023] Open
Abstract
An organic matrix consisting of a protein-polysaccharide complex is generally accepted as an important medium for the calcification process. While the role this "calcified organic matrix" plays in the calcification process has long been appreciated, the complex mixture of proteins that is induced and assembled during the mineral phase of calcification remains uncharacterized in many organisms. Thus, we investigated organic matrices from the calcitic sclerites of a soft coral, Sinularia sp., and used a proteomic approach to identify the functional matrix proteins that might be involved in the biocalcification process. We purified eight organic matrix proteins and performed in-gel digestion using trypsin. The tryptic peptides were separated by nano-liquid chromatography (nano-LC) and analyzed by tandem mass spectrometry (MS/MS) using a matrix-assisted laser desorption/ionization (MALDI) - time-of-flight-time-of-flight (TOF-TOF) mass spectrometer. Periodic acid Schiff staining of an SDS-PAGE gel indicated that four proteins were glycosylated. We identified several proteins, including a form of actin, from which we identified a total of 183 potential peptides. Our findings suggest that many of those peptides may contribute to biocalcification in soft corals.
Collapse
Affiliation(s)
- M Azizur Rahman
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, München, Germany.
| | | | | | | |
Collapse
|
16
|
Marie B, Jackson DJ, Ramos-Silva P, Zanella-Cléon I, Guichard N, Marin F. The shell-forming proteome ofLottia giganteareveals both deep conservations and lineage-specific novelties. FEBS J 2012; 280:214-32. [DOI: 10.1111/febs.12062] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 11/01/2012] [Accepted: 11/07/2012] [Indexed: 12/31/2022]
Affiliation(s)
- Benjamin Marie
- UMR 6282 (ex 5561) CNRS Biogéosciences; Université de Bourgogne; Dijon; France
| | - Daniel J. Jackson
- Courant Research Centre Geobiology; Georg-August University of Göttingen; Göttingen; Germany
| | | | | | - Nathalie Guichard
- UMR 6282 (ex 5561) CNRS Biogéosciences; Université de Bourgogne; Dijon; France
| | - Frédéric Marin
- UMR 6282 (ex 5561) CNRS Biogéosciences; Université de Bourgogne; Dijon; France
| |
Collapse
|
17
|
Ishikawa HO, Xu A, Ogura E, Manning G, Irvine KD. The Raine syndrome protein FAM20C is a Golgi kinase that phosphorylates bio-mineralization proteins. PLoS One 2012; 7:e42988. [PMID: 22900076 PMCID: PMC3416761 DOI: 10.1371/journal.pone.0042988] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 07/16/2012] [Indexed: 01/19/2023] Open
Abstract
Raine syndrome is caused by mutations in FAM20C, which had been reported to encode a secreted component of bone and teeth. We found that FAM20C encodes a Golgi-localized protein kinase, distantly related to the Golgi-localized kinase Four-jointed. Drosophila also encode a Golgi-localized protein kinase closely related to FAM20C. We show that FAM20C can phosphorylate secreted phosphoproteins, including both Casein and members of the SIBLING protein family, which modulate biomineralization, and we find that FAM20C phosphorylates a biologically active peptide at amino acids essential for inhibition of biomineralization. We also identify autophosphorylation of FAM20C, and characterize parameters of FAM20C’s kinase activity, including its Km, pH and cation dependence, and substrate specificity. The biochemical properties of FAM20C match those of an enzymatic activity known as Golgi casein kinase. Introduction of point mutations identified in Raine syndrome patients into recombinant FAM20C impairs its normal localization and kinase activity. Our results identify FAM20C as a kinase for secreted phosphoproteins and establish a biochemical basis for Raine syndrome.
Collapse
Affiliation(s)
- Hiroyuki O. Ishikawa
- Graduate School of Science, Chiba University, Chiba-shi, Chiba, Japan
- Howard Hughes Medical Institute, Waksman Institute and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Aiguo Xu
- Howard Hughes Medical Institute, Waksman Institute and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Eri Ogura
- Graduate School of Science, Chiba University, Chiba-shi, Chiba, Japan
| | - Gerard Manning
- Razavi Newman Center for Bioinformatics, Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Kenneth D. Irvine
- Howard Hughes Medical Institute, Waksman Institute and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
- * E-mail:
| |
Collapse
|
18
|
Debreuil J, Tambutté É, Zoccola D, Deleury E, Guigonis JM, Samson M, Allemand D, Tambutté S. Molecular cloning and characterization of first organic matrix protein from sclerites of red coral, Corallium rubrum. J Biol Chem 2012; 287:19367-76. [PMID: 22505718 PMCID: PMC3365975 DOI: 10.1074/jbc.m112.352005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 04/12/2012] [Indexed: 11/30/2022] Open
Abstract
We report here for the first time the isolation and characterization of a protein from the organic matrix (OM) of the sclerites of the alcyonarian, Corallium rubrum. This protein named scleritin is one of the predominant proteins extracted from the EDTA-soluble fraction of the OM. The entire open reading frame (ORF) was obtained by comparing amino acid sequences from de novo mass spectrometry and Edman degradation with an expressed sequence tag library dataset of C. rubrum. Scleritin is a secreted basic phosphorylated protein which exhibits a short amino acid sequence of 135 amino acids and a signal peptide of 20 amino acids. From specific antibodies raised against peptide sequences of scleritin, we obtained immunolabeling of scleroblasts and OM of the sclerites which provides information on the biomineralization pathway in C. rubrum.
Collapse
Affiliation(s)
- Julien Debreuil
- From the Centre Scientifique de Monaco, Avenue Saint-Martin, MC-98000, Monaco
| | - Éric Tambutté
- From the Centre Scientifique de Monaco, Avenue Saint-Martin, MC-98000, Monaco
| | - Didier Zoccola
- From the Centre Scientifique de Monaco, Avenue Saint-Martin, MC-98000, Monaco
| | - Emeline Deleury
- the Institut Sophia Agrobiotech (ISA) INRA 1355, CNRS 7254, 400 route des Chappes, Sophia-Antipolis F-06903, France
- the Université de Nice-Sophia Antipolis, Nice F-06107, France
| | - Jean-Marie Guigonis
- the Laboratoire Transporteur en Imagerie et Radiothérapie Oncologique, Commissariat à l'Energie Atomique, Nice F-06107, France
- the Faculté de Médecine, Université de Nice-Sophia Antipolis, Nice F-06107, France
- the Centre Antoine Lacassagne, Nice F-06107, France, and
| | - Michel Samson
- the Équipe Région Institut National de la Santé et de la Recherche Medicale 21/ Équipe Associée 4319, Faculté de Médecine, Université de Nice-Sophia Antipolis, Nice F-06107, France
| | - Denis Allemand
- From the Centre Scientifique de Monaco, Avenue Saint-Martin, MC-98000, Monaco
| | - Sylvie Tambutté
- From the Centre Scientifique de Monaco, Avenue Saint-Martin, MC-98000, Monaco
| |
Collapse
|
19
|
Veis A. Organic matrix-related mineralization of sea urchin spicules, spines, test and teeth. FRONT BIOSCI-LANDMRK 2011; 16:2540-60. [PMID: 21622194 PMCID: PMC3516302 DOI: 10.2741/3871] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The camarodont echinoderms have five distinct mineralized skeletal elements: embryonic spicules, mature test, spines, lantern stereom and teeth. The spicules are transient structural elements whereas the spines, and test plates are permanent. The teeth grow continuously. The mineral is a high magnesium calcite, but the magnesium content is different in each type of skeletal element, varying from 5 to 40 mole% Mg. The organic matrix creates the spaces and environments for crystal initiation and growth. The detailed mechanisms of crystal regulation are not known, but acidic and phosphorylated matrix proteins may be of special importance. Biochemical studies, sequencing of the complete genome, and high-throughput proteomic analysis have not yet provided insight into the mechanisms of crystallization, calcite composition, and orientation applicable to all skeletal elements. The embryonic spicules are not representative of the mature skeletal elements. The next phase of research will have to focus on the specific localization of the proteins and individual biochemistries of each system with regard to mineral content and placement.
Collapse
Affiliation(s)
- Arthur Veis
- Feinberg School of Medicine, Northwestern University, Department of Cell and Molecular Biology, 303 E. Chicago Avenue, Chicago, Illinois 60611, USA.
| |
Collapse
|
20
|
Radulovic M, Godovac-Zimmermann J. Proteomic approaches to understanding the role of the cytoskeleton in host-defense mechanisms. Expert Rev Proteomics 2011; 8:117-26. [PMID: 21329431 DOI: 10.1586/epr.10.91] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The cytoskeleton is a cellular scaffolding system whose functions include maintenance of cellular shape, enabling cellular migration, division, intracellular transport, signaling and membrane organization. In addition, in immune cells, the cytoskeleton is essential for phagocytosis. Following the advances in proteomics technology over the past two decades, cytoskeleton proteome analysis in resting and activated immune cells has emerged as a possible powerful approach to expand our understanding of cytoskeletal composition and function. However, so far there have only been a handful of studies of the cytoskeleton proteome in immune cells. This article considers promising proteomics strategies that could augment our understanding of the role of the cytoskeleton in host-defense mechanisms.
Collapse
Affiliation(s)
- Marko Radulovic
- Division of Medicine, University College London, 5 University Street, London WC1E 6JF, UK.
| | | |
Collapse
|
21
|
Adomako-Ankomah A, Ettensohn CA. P58-A and P58-B: novel proteins that mediate skeletogenesis in the sea urchin embryo. Dev Biol 2011; 353:81-93. [PMID: 21362416 DOI: 10.1016/j.ydbio.2011.02.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 02/17/2011] [Accepted: 02/18/2011] [Indexed: 01/17/2023]
Abstract
During sea urchin embryogenesis, the skeleton is produced by primary mesenchyme cells (PMCs). PMCs undergo a sequence of morphogenetic behaviors that includes ingression, directed migration, and cell-cell fusion. Ultimately, PMCs deposit the calcite-containing biomineral that forms the endoskeleton of the late embryo and early larva. The endoskeleton has a stereotypical structure and is the major determinant of the distinctive, angular shape of the larva. Although many candidate biomineralization proteins have been identified, functional data concerning these proteins are scant. Here, we identify and characterize two new biomineralization genes, p58-a and p58-b. We show that these two genes are highly conserved in Strongylocentrotus purpuratus and Lytechinus variegatus, two sea urchin species whose ancestors diverged approximately 100 mya. The p58-a and p58-b genes lie in tandem on the chromosome, suggesting that one of the two genes arose via a gene duplication event. The two genes encode closely related, type I transmembrane proteins. We have established by whole mount in situ hybridization that p58-a and p58-b are expressed specifically in the PMCs in both species. Knockdown of either gene by morpholino antisense oligonucleotides leads to profound defects in skeletogenesis, although skeletal elements are not completely eliminated. The P58-A and P58-B proteins do not appear to play a role in the specification, directed migration or differentiation of the PMCs, but most likely are directly involved in biomineralization during sea urchin embryonic development.
Collapse
Affiliation(s)
- Ashrifia Adomako-Ankomah
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | | |
Collapse
|
22
|
Yang L, Killian CE, Kunz M, Tamura N, Gilbert PUPA. Biomineral nanoparticles are space-filling. NANOSCALE 2011; 3:603-9. [PMID: 21082124 DOI: 10.1039/c0nr00697a] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Sea urchin biominerals have been shown to form from aggregating nanoparticles of amorphous calcium carbonate (ACC), which then crystallize into macroscopic single crystals of calcite. Here we measure the surface areas of these biominerals and find them to be comparable to those of space-filling macroscopic geologic calcite crystals. These biominerals differ from synthetic mesocrystals, which are invariably porous. We propose that space-filling ACC is the structural precursor for echinoderm biominerals.
Collapse
Affiliation(s)
- Li Yang
- Earth Science Division, Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
| | | | | | | | | |
Collapse
|
23
|
Zhou HY, Salih E, Glimcher MJ. The isolation and characterization of glycosylated phosphoproteins from herring fish bones. J Biol Chem 2010; 285:36170-8. [PMID: 20833721 DOI: 10.1074/jbc.m110.146910] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Past studies of bone extracellular matrix phosphoproteins such as osteopontin and bone sialoprotein have yielded important biological information regarding their role in calcification and the regulation of cellular activity. Most of these studies have been limited to proteins extracted from mammalian and avian vertebrates and nonvertebrates. The present work describes the isolation and purification of two major highly glycosylated and phosphorylated extracellular matrix proteins of 70 and 22 kDa from herring fish bones. The 70-kDa phosphoprotein has some characteristics of osteopontin with respect to amino acid composition and susceptibility to thrombin cleavage. Unlike osteopontin, however, it was found to contain high levels of sialic acid similar to bone sialoprotein. The 22-kDa protein has very different properties such as very high content of phosphoserine (∼270 Ser(P) residues/1000 amino acid residues), Ala, and Asx residues. The N-terminal amino acid sequence analysis of both the 70-kDa (NPIMA(M)ETTS(M)DSKVNPLL) and the 22-kDa (NQDMAMEASSDPEAA) fish phosphoproteins indicate that these unique amino acid sequences are unlike any published in protein databases. An enzyme-linked immunosorbent assay revealed that the 70-kDa phosphoprotein was present principally in bone and in calcified scales, whereas the 22-kDa phosphoprotein was detected only in bone. Immunohistological analysis revealed diffusely positive immunostaining for both the 70- and 22-kDa phosphoproteins throughout the matrix of the bone. Overall, this work adds additional support to the concept that the mechanism of biological calcification has common evolutionary and fundamental bases throughout vertebrate species.
Collapse
Affiliation(s)
- Hai-Yan Zhou
- Laboratory for the Study of Skeletal Disorders and Rehabilitation, Department of Orthopedic Surgery, Harvard Medical School and Children's Hospital Boston, Boston, Massachusetts 02115-5737, USA
| | | | | |
Collapse
|
24
|
Mann K, Wilt FH, Poustka AJ. Proteomic analysis of sea urchin (Strongylocentrotus purpuratus) spicule matrix. Proteome Sci 2010; 8:33. [PMID: 20565753 PMCID: PMC2909932 DOI: 10.1186/1477-5956-8-33] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Accepted: 06/17/2010] [Indexed: 01/15/2023] Open
Abstract
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.
Collapse
Affiliation(s)
- Karlheinz Mann
- Max-Planck-Institut für Biochemie, Abteilung Proteomics und Signaltransduktion, D-82152 Martinsried, Am Klopferspitz 18, Germany
| | - Fred H Wilt
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720-3200, USA
| | - Albert J Poustka
- Max-Planck-Institut für Molekulare Genetik, Evolution and Development Group, D-14195 Berlin, Ihnestrasse 73, Germany
| |
Collapse
|