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Jin C, Cheng K, Jiang R, Zhang Y, Luo W. A Novel Kunitz-Type Serine Protease Inhibitor (HcKuSPI) is Involved in Antibacterial Defense in Innate Immunity and Participates in Shell Formation of Hyriopsis cumingii. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:37-49. [PMID: 38117374 DOI: 10.1007/s10126-023-10275-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023]
Abstract
Serine protease inhibitors (SPIs) are abundantly reported for its inhibition against specific proteases involved in the immune responses, but SPI data related to calcareous shells are scarce. Previously, our research group has reported the proteome analysis of non-nucleated pearl powder, and a candidate matrix protein containing two Kunitz domains in the acid soluble fraction caught our attention. In the present study, the full-length cDNA sequence of HcKuSPI was obtained from Hyriopsis cumingii. HcKuSPI was specifically expressed in the mantle, with hybridization signals mainly concentrated to dorsal epithelial cells at the mantle edge and weak signals at the mantle pallium, suggesting HcKuSPI was involved in shell formation. HcKuSPI expression in the mantle was upregulated after Aeromonas hydrophila and Staphylococcus aureus challenge to extrapallial fluids (EPFs). A glutathione S transferase (GST)-HcKuSPI recombinant protein showed strong inhibitory activity against the proteases, trypsin and chymotrypsin. Moreover, HcKuSPI expression in an experimental group was significantly higher when compared with a control group during pellicle growth and crystal deposition in shell regeneration processes, while the organic shell framework of newborn prisms and nacre tablets was completely destroyed after HcKuSPI RNA interference (RNAi). Therefore, HcKuSPI secreted by the mantle may effectively neutralize excess proteases and bacterial proteases in the EPF during bacterial infection and could prevent matrix protein extracellular degradation by suppressing protease proteolytic activity, thereby ensuring a smooth shell biomineralization. In addition, GST-HcKuSPI was also crucial for crystal morphology regulation. These results have important implications for our understanding of the potential roles of SPIs during shell biomineralization.
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Affiliation(s)
- Can Jin
- School of Life and Environmental Sciences, Shaoxing University, Shaoxing, 312000, People's Republic of China
| | - Kang Cheng
- School of Life and Environmental Sciences, Shaoxing University, Shaoxing, 312000, People's Republic of China
| | - Rui Jiang
- School of Life and Environmental Sciences, Shaoxing University, Shaoxing, 312000, People's Republic of China
| | - Yihang Zhang
- School of Life and Environmental Sciences, Shaoxing University, Shaoxing, 312000, People's Republic of China
| | - Wen Luo
- School of Life and Environmental Sciences, Shaoxing University, Shaoxing, 312000, People's Republic of China.
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Sleight VA. Cell type and gene regulatory network approaches in the evolution of spiralian biomineralisation. Brief Funct Genomics 2023; 22:509-516. [PMID: 37592885 PMCID: PMC10658180 DOI: 10.1093/bfgp/elad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 07/10/2023] [Accepted: 07/20/2023] [Indexed: 08/19/2023] Open
Abstract
Biomineralisation is the process by which living organisms produce hard structures such as shells and bone. There are multiple independent origins of biomineralised skeletons across the tree of life. This review gives a glimpse into the diversity of spiralian biominerals and what they can teach us about the evolution of novelty. It discusses different levels of biological organisation that may be informative to understand the evolution of biomineralisation and considers the relationship between skeletal and non-skeletal biominerals. More specifically, this review explores if cell type and gene regulatory network approaches could enhance our understanding of the evolutionary origins of biomineralisation.
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Affiliation(s)
- Victoria A Sleight
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
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3
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Min Y, Li Q, Yu H. Characterization of larval shell formation and CgPOU2F1, CgSox5, and CgPax6 gene expression during shell morphogenesis in Crassostrea gigas. Comp Biochem Physiol B Biochem Mol Biol 2023; 263:110783. [PMID: 35926704 DOI: 10.1016/j.cbpb.2022.110783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022]
Abstract
Shell formation is a dynamic process involving organic matrix secretion and calcification. In this study, we characterized shell morphogenesis during larval development in Crassostrea gigas. Using scanning electron microscopy (SEM) and fluorescence staining, we demonstrated that shell field, the first morphologically distinguishable shell-forming tissue, became visible soon after enlargement of the blastopore at the anterior end of the trochophore. Shell organic matrix namely protein polysaccharides and calcified structure appeared as a slit at the dorsal side of the embryo. The early shell field began to extend along the dorsal side of the trochophore larvae, and became a saddle shaped shell field that gave rise to the prodissoconch I embryonic shell in the early D-shaped larvae. Subsequently, prodissoconch II shell was formed in the late D-shaped larvae with a characteristic appearance of growth lines. To identify gene expression markers for studying shell formation, we isolated three potential larval shell formation genes CgPOU2F1, CgSox5, and CgPax6 and analyzed their expression during shell morphogenesis. The three potential shell formation genes possessed a similar pattern of expression. Their expression was detected in the shell gland and shell field regions in early D-shaped larvae, hereafter, their expression was detected at the larval mantle edge in the calcified shell stages. Together, these studies provide knowledge of shell morphogenesis in pacific oyster and molecular markers for studying the molecular regulation of biomineralization and shell formation.
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Affiliation(s)
- Yue Min
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Hong Yu
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
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4
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Khurshid B, Jackson DJ, Engilberge S, Motreuil S, Broussard C, Thomas J, Immel F, Harrington MJ, Crowley PB, Vielzeuf D, Perrin J, Marin F. Molecular characterization of accripin11, a soluble shell protein with an acidic C-terminus, identified in the prismatic layer of the Mediterranean fan mussel Pinna nobilis (Bivalvia, Pteriomorphia). FEBS Open Bio 2022; 13:10-25. [PMID: 36219517 PMCID: PMC9808598 DOI: 10.1002/2211-5463.13497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/23/2022] [Accepted: 10/10/2022] [Indexed: 01/07/2023] Open
Abstract
We have identified a novel shell protein, accripin11, as a major soluble component of the calcitic prisms of the fan mussel Pinna nobilis. Initially retrieved from a cDNA library, its full sequence is confirmed here by transcriptomic and proteomic approaches. The sequence of the mature protein is 103 residues with a theoretical molecular weight of 11 kDa and is moderately acidic (pI 6.74) except for its C-terminus which is highly enriched in aspartic acid. The protein exhibits a peculiar cysteine pattern in its central domain. The full sequence shares similarity with six other uncharacterized molluscan shell proteins from the orders Ostreida, Pteriida and Mytilida, all of which are pteriomorphids and produce a phylogenetically restricted pattern of nacro-prismatic shell microstructures. This suggests that accripin11 is a member of a family of clade-specific shell proteins. A 3D model of accripin11 was predicted with AlphaFold2, indicating that it possesses three short alpha helices and a disordered C-terminus. Recombinant accripin11 was tested in vitro for its ability to influence the crystallization of CaCO3 , while a polyclonal antibody was able to locate accripin11 to prismatic extracts, particularly in the acetic acid-soluble matrix. The putative functions of accripin11 are further discussed in relation to shell biomineralization.
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Affiliation(s)
- Benazir Khurshid
- Laboratoire Biogéosciences, UMR CNRS‐EPHE 6282Université de Bourgogne – Franche‐ComtéDijonFrance,Synchrotron SOLEILBeamline ANATOMIXGif‐sur‐YvetteFrance
| | | | - Sylvain Engilberge
- Structural Biology GroupEuropean Synchrotron Radiation FacilityGrenobleFrance
| | - Sébastien Motreuil
- Laboratoire Biogéosciences, UMR CNRS‐EPHE 6282Université de Bourgogne – Franche‐ComtéDijonFrance
| | | | - Jérôme Thomas
- Laboratoire Biogéosciences, UMR CNRS‐EPHE 6282Université de Bourgogne – Franche‐ComtéDijonFrance
| | - Françoise Immel
- Chrono‐Environnement, UMR 6249 CNRSUniversité de Bourgogne Franche‐ComtéBesançonFrance
| | | | - Peter B. Crowley
- School of Biological and Chemical SciencesNational University of IrelandGalwayIreland
| | | | | | - Frédéric Marin
- Laboratoire Biogéosciences, UMR CNRS‐EPHE 6282Université de Bourgogne – Franche‐ComtéDijonFrance
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Cavallo A, Clark MS, Peck LS, Harper EM, Sleight VA. Evolutionary conservation and divergence of the transcriptional regulation of bivalve shell secretion across life-history stages. ROYAL SOCIETY OPEN SCIENCE 2022; 9:221022. [PMID: 36569229 PMCID: PMC9768464 DOI: 10.1098/rsos.221022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/13/2022] [Indexed: 06/17/2023]
Abstract
Adult molluscs produce shells with diverse morphologies and ornamentations, different colour patterns and microstructures. The larval shell, however, is a phenotypically more conserved structure. How do developmental and evolutionary processes generate varying diversity at different life-history stages within a species? Using live imaging, histology, scanning electron microscopy and transcriptomic profiling, we have described shell development in a heteroconchian bivalve, the Antarctic clam, Laternula elliptica, and compared it to adult shell secretion processes in the same species. Adult downstream shell genes, such as those encoding extracellular matrix proteins and biomineralization enzymes, were largely not expressed during shell development. Instead, a development-specific downstream gene repertoire was expressed. Upstream regulatory genes such as transcription factors and signalling molecules were largely conserved between developmental and adult shell secretion. Comparing heteroconchian data with recently reported pteriomorphian larval shell development data suggests that, despite being phenotypically more conserved, the downstream effectors constituting the larval shell 'tool-kit' may be as diverse as that of adults. Overall, our new data suggest that a larval shell formed using development-specific downstream effector genes is a conserved and ancestral feature of the bivalve lineage, and possibly more broadly across the molluscs.
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Affiliation(s)
- Alessandro Cavallo
- Biodiversity, Evolution and Adaptation Team, British Antarctic Survey, Cambridge CB3 0ET, UK
| | - Melody S. Clark
- Biodiversity, Evolution and Adaptation Team, British Antarctic Survey, Cambridge CB3 0ET, UK
| | - Lloyd S. Peck
- Biodiversity, Evolution and Adaptation Team, British Antarctic Survey, Cambridge CB3 0ET, UK
| | - Elizabeth M. Harper
- Department of Earth Sciences, University of Cambridge, Cambridge CB2 1TN, UK
| | - Victoria A. Sleight
- Biodiversity, Evolution and Adaptation Team, British Antarctic Survey, Cambridge CB3 0ET, UK
- Department of Zoology, University of Cambridge, Cambridge CB2 1TN, UK
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, UK
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6
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Batzel GO, Moreno BK, Lopez LS, Nguyen CK, Livingston BT, Joester D, Lyons DC. Proteomic and Transcriptomic Analyses in the Slipper Snail Crepidula
fornicata Uncover Shell Matrix Genes Expressed During Adult and Larval Biomineralization. Integr Org Biol 2022; 4:obac023. [PMID: 35968217 PMCID: PMC9365450 DOI: 10.1093/iob/obac023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/18/2022] [Indexed: 11/12/2022] Open
Abstract
The gastropod shell is a composite composed of minerals and shell matrix proteins (SMPs). SMPs have been identified by proteomics in many molluscs, but few have been studied in detail. Open questions include (1) what gene regulatory networks regulate SMP expression, (2) what roles individual SMPs play in biomineralization, and (3) how the complement of SMPs changes over development. These questions are best addressed in a species in which gene perturbation studies are available; one such species is the slipper snail, Crepidula fornicata. Here, SEM and pXRD analysis demonstrated that the adult shell of C. fornicata exhibits crossed lamellar microstructure and is composed of aragonite. Using high-throughput proteomics we identified 185 SMPs occluded within the adult shell. Over half of the proteins in the shell proteome have known biomineralization domains, while at least 10% have no homologs in public databases. Differential gene expression analysis identified 20 SMP genes that are up-regulated in the shell-producing mantle tissue. Over half of these 20 SMPs are expressed during development with two, CfSMP1 and CfSMP2, expressed exclusively in the shell gland. Together, the description of the shell microstructure and a list of SMPs now sets the stage for studying the consequences of SMP gene knockdowns in molluscs.
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Affiliation(s)
- G O Batzel
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , UCSD, La Jolla, CA 92037, USA
| | - B K Moreno
- Department of Materials Science and Engineering, Northwestern University , Evanston, IL 60208, USA
| | - L S Lopez
- Department of Biological Sciences, California State University , Long Beach, CA 90802, USA
| | - C K Nguyen
- Department of Biological Sciences, California State University , Long Beach, CA 90802, USA
| | - B T Livingston
- Department of Biological Sciences, California State University , Long Beach, CA 90802, USA
| | - D Joester
- Department of Materials Science and Engineering, Northwestern University , Evanston, IL 60208, USA
| | - D C Lyons
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , UCSD, La Jolla, CA 92037, USA
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Rivera-Pérez C, Arroyo-Loranca RG, Hernández-Saavedra NY. An acidic protein, Hf15, from Haliotis fulgens involved in biomineralization. Comp Biochem Physiol A Mol Integr Physiol 2022; 272:111276. [PMID: 35853523 DOI: 10.1016/j.cbpa.2022.111276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/20/2022] [Accepted: 07/13/2022] [Indexed: 11/16/2022]
Abstract
Biomineralization leads to the hardening of mineralized materials, such as the shell of Mollusk, to fulfill a wide range of functions, such as (but not limited to) skeletal support, protection of the soft tissues, navigation, etc. The study of the proteins responsible for this process, shell matrix proteins (SMPs), allows addressing questions related to structure-function relationship and to the mechanism of mineral formation, which is limited in gastropod species. In this study, a low molecular weight protein was isolated from the insoluble fraction after decalcification with acetic acid of the shell of Haliotis fulgens and, named Hf15. The unglycosylated protein has a theoretical molecular weight of 15 kDa, it possesses calcium and chiting binding properties. Hf15 can precipitate calcium carbonate in vitro in presence of different salts. Analysis by LC-MS of the five peptide sequences of Hf15 generated by trypsinization revealed that two peptides displayed homology to an uncharacterized protein 3-like from Haliotis rufescens, Haliotis asinia and H. sorenseni. The results obtained indicated that Hf15 is a novel SMP involved in shell mineralization in Haliotis fulgens.
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Affiliation(s)
| | - Raquel G Arroyo-Loranca
- Fisheries Ecology, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, Mexico
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Venter L, Alfaro AC, Van Nguyen T, Lindeque JZ. Metabolite profiling of abalone (Haliotis iris) energy metabolism: a Chatham Islands case study. Metabolomics 2022; 18:52. [PMID: 35829802 PMCID: PMC9279229 DOI: 10.1007/s11306-022-01907-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 06/15/2022] [Indexed: 11/09/2022]
Abstract
INTRODUCTION The Chatham Islands has some of the most prized black-footed abalone (Haliotis iris) beds in New Zealand. This well-managed fishery includes restrictions on catch and size limits, selective fishing methods, and shellfish management. However, recent declines in biomass and growth parameters have prompted omics research to characterise the biological responses of abalone, potentially contributing towards animal management strategies. OBJECTIVES The aim of this study was to characterise the metabolite profiles of slow and fast growing, juvenile and adult abalone, relating to metabolites supporting energy metabolism. METHODS A gas chromatography-mass spectrometry metabolite profiling, applying methyl chloroformate alkylation, was performed on juvenile and adult abalone samples collected from Point Durham and Wharekauri sites, Chatham Islands, New Zealand. RESULTS The results obtained from haemolymph and muscle samples indicated that abalone from the fast-growing area, Wharekauri, fuelled metabolic functions via carbohydrate sources, providing energy for fatty acid and amino acid synthesis. Conversely, higher amino acid levels were largely utilised to promote growth in this population. The metabolism of juvenile abalone favoured anabolism, where metabolites were diverted from glycolysis and the tricarboxylic acid cycle, and used for the production of nucleotides, amino acids and fatty acids. CONCLUSIONS This research provides unique physiological insights towards abalone populations supporting the use of metabolomics as a tool to investigate metabolic processes related to growth. This work sets the stage for future work aimed at developing biomarkers for growth and health monitoring to support a growing and more sustainably abalone fishery.
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Affiliation(s)
- Leonie Venter
- Aquaculture Biotechnology Research Group, Department of Environmental Science, School of Science, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | - Andrea C Alfaro
- Aquaculture Biotechnology Research Group, Department of Environmental Science, School of Science, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand.
| | - Thao Van Nguyen
- Aquaculture Biotechnology Research Group, Department of Environmental Science, School of Science, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Jeremie Zander Lindeque
- Human Metabolomics, North West University, Potchefstroom Campus, Private Bag X 6001, Potchefstroom, 2520, South Africa
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The proteomics of the freshwater pearl powder: Insights from biomineralization to biomedical application. J Proteomics 2022; 265:104665. [PMID: 35753678 DOI: 10.1016/j.jprot.2022.104665] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/30/2022] [Accepted: 06/15/2022] [Indexed: 11/24/2022]
Abstract
The freshwater pearl is one kind of valuable organic jewelry and traditional Chinese medicine (TCM). However, the molecular basis of matrix protein in pearl biomineralization and biomedical applications are largely unknown to date. In this study, the matrix proteins of water-soluble matrix, acid-soluble matrix and acid-insoluble matrix from the freshwater seedless pearl powder were detected using liquid chromatography-tandem mass spectrometry (LC-MS/MS) respectively, and identified against the transcriptomic database of the pearl sac. The results showed that a total of 190 proteins were identified in pearl proteomics, which was divided into eight categories by their potential biomineralization functions. The composition of pearl matrix proteins and the high frequency conserved domains like carbonic anhydrase, von Willebrand factor type A, tyrosinase and chitin binding 2 in protein sequences, implying that the "chitin-silk fibroin gel proteins-acidic macromolecules" model was suitable for description the pearl biomineralization process. Meanwhile, ninety-one of pearl matrix proteins could be classified into seven categories by their potential medical functions including wound healing, osteogenic property, antioxidant activity, neuro-regulation effects, skin lightening effect, anti-inflammatory and anti-apoptotic effects and other immunomodulatory property. In general, these results provided valuable new insights into not only the diversity of pearl matrix protein for mollusc biomineralization, but the molecular basis of pearl matrix proteins responsible for their diverse biological properties in TCM application. SIGNIFICANCE: The significance of this study included the following points.
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Salamanca-Díaz DA, Ritschard EA, Schmidbaur H, Wanninger A. Comparative Single-Cell Transcriptomics Reveals Novel Genes Involved in Bivalve Embryonic Shell Formation and Questions Ontogenetic Homology of Molluscan Shell Types. Front Cell Dev Biol 2022; 10:883755. [PMID: 35813198 PMCID: PMC9261976 DOI: 10.3389/fcell.2022.883755] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/19/2022] [Indexed: 12/29/2022] Open
Abstract
Mollusks are known for their highly diverse repertoire of body plans that often includes external armor in form of mineralized hardparts. Representatives of the Conchifera, one of the two major lineages that comprises taxa which originated from a uni-shelled ancestor (Monoplacophora, Gastropoda, Cephalopoda, Scaphopoda, Bivalvia), are particularly relevant regarding the evolution of mollusk shells. Previous studies have found that the shell matrix of the adult shell (teleoconch) is rapidly evolving and that the gene set involved in shell formation is highly taxon-specific. However, detailed annotation of genes expressed in tissues involved in the formation of the embryonic shell (protoconch I) or the larval shell (protoconch II) are currently lacking. Here, we analyzed the genetic toolbox involved in embryonic and larval shell formation in the quagga mussel Dreissena rostriformis using single cell RNA sequencing. We found significant differences in genes expressed during embryonic and larval shell secretion, calling into question ontogenetic homology of these transitory bivalve shell types. Further ortholog comparisons throughout Metazoa indicates that a common genetic biomineralization toolbox, that was secondarily co-opted into molluscan shell formation, was already present in the last common metazoan ancestor. Genes included are engrailed, carbonic anhydrase, and tyrosinase homologs. However, we found that 25% of the genes expressed in the embryonic shell field of D. rostriformis lack an ortholog match with any other metazoan. This indicates that not only adult but also embryonic mollusk shells may be fast-evolving structures. We raise the question as to what degree, and on which taxonomic level, the gene complement involved in conchiferan protoconch formation may be lineage-specific or conserved across taxa.
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Affiliation(s)
- David A. Salamanca-Díaz
- Unit for Integrative Zoology, Department of Evolutionary Biology, University of Vienna, Vienna, Austria
| | - Elena A. Ritschard
- Division of Molecular Evolution and Development, Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Hannah Schmidbaur
- Division of Molecular Evolution and Development, Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Andreas Wanninger
- Unit for Integrative Zoology, Department of Evolutionary Biology, University of Vienna, Vienna, Austria
- *Correspondence: Andreas Wanninger,
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11
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Xing H, Yang F, Sun S, Pan P, Wang H, Wang Y, Chen J. Green efficient ultrasonic-assisted extraction of abalone nacre water-soluble organic matrix for bioinspired enamel remineralization. Colloids Surf B Biointerfaces 2022; 212:112336. [PMID: 35051793 DOI: 10.1016/j.colsurfb.2022.112336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 12/31/2021] [Accepted: 01/12/2022] [Indexed: 11/25/2022]
Abstract
Reconstructing enamel-like hydroxyapatite structures on damaged teeth remains a great challenge in the materials science and dentistry due to its highly ordered hierarchical microstructure. Inspired by the mineralization of mollusk nacre in nature, abalone nacre water-soluble organic matrix (WSM) was isolated successfully though an ultrasonic-assisted water extraction (UWE) strategy with nondestructive activity and high-quality extraction for simulating the process of tooth hard tissue mineralization. Results showed that the UWE strategy significantly increased the protein yield from 7.60% to 9.60% and improved the polysaccharide yield from 2.59% to 3.34%, respectively, indicating its excellent extraction efficiency of WSM. Noteworthily, the smallest averaged particle size (~155 nm) of WSM were obtained at an ultrasound time of 6 h, whereas the highest absolute values (~ -32 mV) of zeta potential was produced. Moreover, it was proved that WSM could induce the growth of enamel-like hydroxyapatite crystals to further facilitate biomimetic remineralization of the demineralized enamel and restore its continuous and smooth surface structure in vitro. Besides, the hardness (4.37 ± 0.07 GPa) and modulus of elasticity (84.80 ± 1.49 GPa) of the WSM-repaired enamel was similar to that of native enamel, indicating superior mechanical properties after repair. Herein, it provides a promising green, efficient strategy for the remineralization of damaged enamel and high value utilization of waste abalone shells.
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Affiliation(s)
- Huaran Xing
- Marine College, Shandong University, Weihai 264209, China
| | - Faming Yang
- Marine College, Shandong University, Weihai 264209, China
| | - Shengjun Sun
- Shandong Provincial Key Laboratory of Oral Biomedicine, College of Stomatology, Shandong University, Jinan 250021, China.
| | - Panpan Pan
- Marine College, Shandong University, Weihai 264209, China; Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration, Wuhan 430022, China.
| | - Hongbo Wang
- Marine College, Shandong University, Weihai 264209, China
| | - Yuxin Wang
- Marine College, Shandong University, Weihai 264209, China
| | - Jingdi Chen
- Marine College, Shandong University, Weihai 264209, China; Shandong Laboratory of Advanced Materials and Green Manufacturing, Yantai 265599, China.
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12
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Feng X, Jiang S, Zhang F, Wang R, Zhao Y, Zeng M. Shell water-soluble matrix protein from oyster shells promoted proliferation, differentiation and mineralization of osteoblasts in vitro and vivo. Int J Biol Macromol 2022; 201:288-297. [PMID: 34998879 DOI: 10.1016/j.ijbiomac.2021.12.168] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 12/27/2021] [Accepted: 12/27/2021] [Indexed: 12/23/2022]
Abstract
Matrix protein is secreted by the membrane of bivalve shellfish to and used to regulate shell biomineralization. In this study, we extracted water-soluble matrix protein (WSMP) from oyster shells to investigate its effects on osteogenic differentiation and mineralization of MC3T3-E1 cells and osteoporosis rats. Our results suggested that WSMP was an acidic glycoprotein by amino acid analysis and secondary structure analysis. In vitro, WSMP could promote osteoblastic proliferation. Moreover, alkaline phosphatase (ALP) and osteocalcin (OCN) were increased, mineralized nodules were increased, and BMP-2 expression was up-regulated. Additionally, in vivo, tartrate-resistant acid phosphatase (TRAP) and Bone alkaline phosphatase (BALP) expressions in the medium-dose and high-dose groups were significantly decreased compared with the model group, while OCN expression was significantly increased. Bone mineral density (BMD) and bone mineral content (BMC) of bone recovered significantly. In summary, WSMP can promote the proliferation, differentiation and mineralization of osteoblasts in vitro and in vivo.
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Affiliation(s)
- Xue Feng
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China
| | - Suisui Jiang
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China
| | - Fan Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China
| | - Runfang Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China
| | - Yuanhui Zhao
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China.
| | - Mingyong Zeng
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China.
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13
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Song N, Li J, Li B, Pan E, Gao J, Ma Y. In vitro crystallization of calcium carbonate mediated by proteins extracted from P. placenta shells. CrystEngComm 2022. [DOI: 10.1039/d2ce00692h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ASM extracted from the shells of P. placenta can stabilize ACC and inhibit secondary nucleation for 10 hours, and an explosive secondary nucleation and quick crystal growth from 50 nm to 10 μm can be finished on the shell surface in one hour.
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Affiliation(s)
- Ningjing Song
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Jiangfeng Li
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Baosheng Li
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Ercai Pan
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Juan Gao
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Yurong Ma
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
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14
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Feng X, Jiang S, Zhang F, Wang R, Zhang T, Zhao Y, Zeng M. Extraction and characterization of matrix protein from pacific oyster ( Crassostrea gigs) shell and its anti-osteoporosis properties in vitro and in vivo. Food Funct 2021; 12:9066-9076. [PMID: 34387295 DOI: 10.1039/d1fo00010a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Matrix protein is a kind of secretory protein that regulates the biomineralization of the bivalve shell. In this study, a water-soluble matrix protein (WSMP) from Pacific oysters (Crassostrea gigs) shell was isolated, and its structure was analyzed in detail, in addition to its anti-osteoporosis activity in vitro and in vivo. Results showed that WSMP was an acidic protein with an apparent molecular mass of 47 and 79 kDa and contained a glycoprotein structure. In vitro, the reduction of Tartrate-resistant acid phosphatase (TRAP) and deoxypyridinoline (DPD) indicated that osteoclast activity was inhibited compared with the model group. Moreover, the increased osteocalcin (OCN) and BMD levels suggested that the high osteoblast activity and bone mineralization was improved. SEM analysis of the femur showed that there were fewer bone pits in experimental groups, which was consistent with the above results. In vivo, WSMP promoted the expression of alkaline phosphatase (ALP) and osteogenic differentiation factor BMP-2 in osteoblasts. In addition, the activity of osteoclasts was inhibited by regulating the process of osteoclast differentiation induced by RANKL. Both in vitro and in vivo studies showed that WSMP could promote osteogenesis and inhibit osteoclast absorption, thus demonstrating their potential applications in osteoporosis.
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Affiliation(s)
- Xue Feng
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China.
| | - Suisui Jiang
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China.
| | - Fan Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China.
| | - Runfang Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China.
| | - Tietao Zhang
- College of Food Science and Engineering, Hainan Tropical Ocean University, Sanya, Hainan 572022, China
| | - Yuanhui Zhao
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China.
| | - Mingyong Zeng
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China.
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15
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Colgan DJ. The potential for using shell proteins in gastropod systematics, assessed in patellogastropod limpets. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
This investigation of the application of shell protein information to gastropod systematics initially utilized available Lottia gigantea sequences and a transcriptome of Patelloida mimula developed here. Levels of differentiation between predicted sequences of reciprocal best-hit potential homologues in P. mimula and L. gigantea suggested that they could be useful within families, and possibly in higher taxa using some shell-associated proteins, particularly the peroxidases. Subsequently, proteomic analyses of the acid-soluble fraction of extractions from 17 shells and five tissue samples were conducted by combined liquid chromatography/mass spectrometry with nano-electrospray ionization. All proteins with abundance more than 1.2% in the L. gigantea shell proteome were identified with 100% confidence in most extractions by SearchGui/PeptideShaker analyses. In total, 259 of 379 peptides predicted from in silico digestion of L. gigantea shell proteins were represented by validated peptide spectrum matches in one or more specimens. Systematics applications were investigated by analysing metrics such as protein coverage by peptides and phylogenetic analyses of peptide presence/absence. The investigation suggested that diagnostic profiles based on fixed presence/absence differences can be used to separate species pairs. However, further development of analytical techniques and accumulation of reference databases is required for realising fully the systematics potential of the shell proteome.
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Affiliation(s)
- Donald James Colgan
- Malacology, Australian Museum Research Institute, The Australian Museum, 1 William St, Sydney 2010, Australia
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16
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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.
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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
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17
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Conci N, Lehmann M, Vargas S, Wörheide G. Comparative Proteomics of Octocoral and Scleractinian Skeletomes and the Evolution of Coral Calcification. Genome Biol Evol 2021; 12:1623-1635. [PMID: 32761183 PMCID: PMC7533068 DOI: 10.1093/gbe/evaa162] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2020] [Indexed: 12/23/2022] Open
Abstract
Corals are the ecosystem engineers of coral reefs, one of the most biodiverse marine ecosystems. The ability of corals to form reefs depends on the precipitation of calcium carbonate (CaCO3) under biological control. However, several mechanisms underlying coral biomineralization remain elusive, for example, whether corals employ different molecular machineries to deposit different CaCO3 polymorphs (i.e., aragonite or calcite). Here, we used tandem mass spectrometry (MS/MS) to compare the proteins occluded in the skeleton of three octocoral and one scleractinian species: Tubipora musica and Sinularia cf. cruciata (calcite sclerites), the blue coral Heliopora coerulea (aragonitic skeleton), and the scleractinian aragonitic Montipora digitata. Reciprocal Blast analysis revealed extremely low overlap between aragonitic and calcitic species, while a core set of proteins is shared between octocorals producing calcite sclerites. However, the carbonic anhydrase CruCA4 is present in the skeletons of both polymorphs. Phylogenetic analysis highlighted several possible instances of protein co-option in octocorals. These include acidic proteins and scleritin, which appear to have been secondarily recruited for calcification and likely derive from proteins playing different functions. Similarities between octocorals and scleractinians included presence of a galaxin-related protein, carbonic anhydrases, and one hephaestin-like protein. Although the first two appear to have been independently recruited, the third appear to share a common origin. This work represents the first attempt to identify and compare proteins associated with coral skeleton polymorph diversity, providing several new research targets and enabling both future functional and evolutionary studies aimed at elucidating the origin and evolution of coral biomineralization.
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Affiliation(s)
- Nicola Conci
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Martin Lehmann
- Department of Biology I-Botany, Biozentrum der LMU München, Planegg-Martinsried, Germany
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany.,SNSB - Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany.,GeoBio-Center LMU, Ludwig-Maximilians-Universität München, München, Germany
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18
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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.
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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
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19
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Le Roy N, Stapane L, Gautron J, Hincke MT. Evolution of the Avian Eggshell Biomineralization Protein Toolkit - New Insights From Multi-Omics. Front Genet 2021; 12:672433. [PMID: 34046059 PMCID: PMC8144736 DOI: 10.3389/fgene.2021.672433] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/08/2021] [Indexed: 11/13/2022] Open
Abstract
The avian eggshell is a remarkable biomineral, which is essential for avian reproduction; its properties permit embryonic development in the desiccating terrestrial environment, and moreover, are critically important to preserve unfertilized egg quality for human consumption. This calcium carbonate (CaCO3) bioceramic is made of 95% calcite and 3.5% organic matrix; it protects the egg contents against microbial penetration and mechanical damage, allows gaseous exchange, and provides calcium for development of the embryonic skeleton. In vertebrates, eggshell occurs in the Sauropsida and in a lesser extent in Mammalia taxa; avian eggshell calcification is one of the fastest known CaCO3 biomineralization processes, and results in a material with excellent mechanical properties. Thus, its study has triggered a strong interest from the researcher community. The investigation of eggshell biomineralization in birds over the past decades has led to detailed characterization of its protein and mineral constituents. Recently, our understanding of this process has been significantly improved using high-throughput technologies (i.e., proteomics, transcriptomics, genomics, and bioinformatics). Presently, more or less complete eggshell proteomes are available for nine birds, and therefore, key proteins that comprise the eggshell biomineralization toolkit are beginning to be identified. In this article, we review current knowledge on organic matrix components from calcified eggshell. We use these data to analyze the evolution of selected matrix proteins and underline their role in the biological toolkit required for eggshell calcification in avian species. Amongst the panel of eggshell-associated proteins, key functional domains are present such as calcium-binding, vesicle-binding and protein-binding. These technical advances, combined with progress in mineral ultrastructure analyses, have opened the way for new hypotheses of mineral nucleation and crystal growth in formation of the avian eggshell, including transfer of amorphous CaCO3 in vesicles from uterine cells to the eggshell mineralization site. The enrichment of multi-omics datasets for bird species is critical to understand the evolutionary context for development of CaCO3 biomineralization in metazoans, leading to the acquisition of the robust eggshell in birds (and formerly dinosaurs).
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Affiliation(s)
| | | | | | - Maxwell T Hincke
- Department of Innovation in Medical Education, University of Ottawa, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
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20
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Nam BH, Kim H, Seol D, Kim H, Noh ES, Kim EM, Noh JK, Kim YO, Park JY, Kwak W. Genotyping-by-Sequencing of the regional Pacific abalone (Haliotis discus) genomes reveals population structures and patterns of gene flow. PLoS One 2021; 16:e0247815. [PMID: 33826655 PMCID: PMC8026068 DOI: 10.1371/journal.pone.0247815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 02/12/2021] [Indexed: 01/05/2023] Open
Abstract
Continuous monitoring of the present genetic status is essential to preserve the genetic resource of wild populations. In this study, we sequenced regional Pacific abalone Haliotis discus samples from three different locations around the Korean peninsula to assess population structure, utilizing Genotyping-by-Sequencing (GBS) method. Using PstI enzyme for genome reduction, we demonstrated the resultant library represented the whole genome region with even spacing, and as a result 16,603 single nucleotide variants (SNVs) were produced. Genetic diversity and population structure were investigated using several methods, and a strong genetic heterogeneity was observed in the Korean abalone populations. Additionally, by comparison of the variant sets among population groups, we were able to discover 26 Korean abalone population-specific SNVs, potentially associated with phenotype differences. This is the first study demonstrating the feasibility of GBS for population genetic study on H. discus. Our results will provide valuable data for the genetic conservation and management of wild abalone populations in Korea and help future GBS studies on the marine mollusks.
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Affiliation(s)
- Bo-Hye Nam
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Hyaekang Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Donghyeok Seol
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Genome, Inc, Seoul, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Genome, Inc, Seoul, Republic of Korea
| | - Eun Soo Noh
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Eun Mi Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Jae Koo Noh
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Young-Ok Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Jung Youn Park
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Woori Kwak
- Genome, Inc, Seoul, Republic of Korea
- * E-mail:
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21
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Liu C, Zhang R. Biomineral proteomics: A tool for multiple disciplinary studies. J Proteomics 2021; 238:104171. [PMID: 33652138 DOI: 10.1016/j.jprot.2021.104171] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/06/2021] [Accepted: 02/21/2021] [Indexed: 12/11/2022]
Abstract
The hard tissues of animals, such as skeletons and teeth, are constructed by a biologically controlled process called biomineralization. In invertebrate animals, biominerals are considered important for their evolutionary success. These biominerals are hieratical biocomposites with excellent mechanical properties, and their formation has intrigued researchers for decades. Although proteins account for ~5 wt% of biominerals, they are critical players in biomineralization. With the development of high-throughput analysis methods, such as proteomics, biomineral protein data are rapidly accumulating, thus necessitating a refined model for biomineralization. This review focuses on biomineral proteomics in invertebrate animals to highlight the diversity of biomineral proteins (generally 40-80 proteins), and the results indicate that biomineralization includes thermodynamic crystal growth as well as intense extracellular matrix activity and/or vesicle transport. Biominerals have multiple functions linked to biological immunity and antipathogen activity. A comparison of proteomes across species and biomineral types showed that von Willebrand factor type A and epidermal growth factor, which frequently couple with other extracellular domains, are the most common domains. Combined with species-specific repetitive low complexity domains, shell matrix proteins can be employed to predict biomineral types. Furthermore, this review discusses the applications of biomineral proteomics in diverse fields, such as tissue regeneration, developmental biology, archeology, environmental science, and material science.
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Affiliation(s)
- Chuang Liu
- College of Oceanography, Hohai University, Xikang Road, Nanjing, Jiangsu 210098, China.
| | - Rongqing Zhang
- Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, 705 Yatai Road, Jiaxing 314006, PR China; College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, China.
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22
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Teh LSX, Poo JST, Boo MV, Chew SF, Ip YK. Using glutamine synthetase 1 to evaluate the symbionts' potential of ammonia assimilation and their responses to illumination in five organs of the giant clam, Tridacna squamosa. Comp Biochem Physiol A Mol Integr Physiol 2021; 255:110914. [PMID: 33540079 DOI: 10.1016/j.cbpa.2021.110914] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/23/2021] [Accepted: 01/25/2021] [Indexed: 11/16/2022]
Abstract
Nitrogen-deficient symbiotic dinoflagellates (zooxanthellae) living inside the fluted giant clam, Tridacna squamosa, need to obtain nitrogen from the host. Glutamine synthetase 1 (GS1) is a cytosolic enzyme that assimilates ammonia into glutamine. We determined the transcript levels of zooxanthellal GS1 (Zoox-GS1), which represented comprehensively GS1 transcripts of Symbiodinium, Cladocopium and Durusdinium, in five organs of T. squamosa. The outer mantle had significantly higher transcript level of Zoox-GS1 than the inner mantle, foot muscle, hepatopancreas and ctenidium, but the transcript ratios of Zoox-GS1 to zooxanthellal form II ribulose-1,5-bisphosphate carboxylase/oxygenase (Zoox-rbcII), which represented the potential of ammonia assimilation relative to the phototrophic potential, were comparable among these five organs. Based on transcript ratios of Zoox-GS1 to zooxanthellal Urease (Zoox-URE), the outer mantle had the highest potential of urea degradation relative to ammonia assimilation among the five organs, probably because urea degradation could furnish CO2 and NH3 for photosynthesis and amino acid synthesis, respectively, in the symbionts therein. The protein abundance of Zoox-GS1 was upregulated in the outer mantle and the inner mantle during illumination. Zoox-GS1 could catalyze light-enhanced glutamine formation using ammonia absorbed from the host or ammonia released through urea degradation in the cytoplasm. The glutamine produced could be used to synthesize other nitrogenous compounds, including amino acids in the cytoplasm or in the plastid of the dinoflagellates. Some of the amino acids synthesized by the symbionts in the inner mantle and foot muscle could be donated to the host to support shell organic matrix formation and muscle production, respectively.
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Affiliation(s)
- Leanne S X Teh
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Jeslyn S T Poo
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Mel V Boo
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Shit F Chew
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore 637616, Republic of Singapore
| | - Yuen K Ip
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore.
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23
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McDougall C, Aguilera F, Shokoohmand A, Moase P, Degnan BM. Pearl Sac Gene Expression Profiles Associated With Pearl Attributes in the Silver-Lip Pearl Oyster, Pinctada maxima. Front Genet 2021; 11:597459. [PMID: 33488672 PMCID: PMC7820862 DOI: 10.3389/fgene.2020.597459] [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: 08/21/2020] [Accepted: 12/07/2020] [Indexed: 11/21/2022] Open
Abstract
Pearls are highly prized biomineralized gemstones produced by molluscs. The appearance and mineralogy of cultured pearls can vary markedly, greatly affecting their commercial value. To begin to understand the role of pearl sacs—organs that form in host oysters from explanted mantle tissues that surround and synthesize pearls—we undertook transcriptomic analyses to identify genes that are differentially expressed in sacs producing pearls with different surface and structural characteristics. Our results indicate that gene expression profiles correlate with different pearl defects, suggesting that gene regulation in the pearl sac contributes to pearl appearance and quality. For instance, pearl sacs that produced pearls with surface non-lustrous calcification significantly down-regulate genes associated with cilia and microtubule function compared to pearl sacs giving rise to lustrous pearls. These results suggest that gene expression profiling can advance our understanding of processes that control biomineralization, which may be of direct value to the pearl industry, particularly in relation to defects that result in low value pearls.
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Affiliation(s)
- Carmel McDougall
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia.,Australian Rivers Institute, Griffith University, Nathan, QLD, Australia
| | - Felipe Aguilera
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Ali Shokoohmand
- Australian Rivers Institute, Griffith University, Nathan, QLD, Australia
| | - Patrick Moase
- Clipper Pearls and Autore Pearling, Broome, WA, Australia
| | - Bernard M Degnan
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia
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24
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Carter OWL, Xu Y, Sadler PJ. Minerals in biology and medicine. RSC Adv 2021; 11:1939-1951. [PMID: 35424161 PMCID: PMC8693805 DOI: 10.1039/d0ra09992a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 12/21/2020] [Indexed: 01/08/2023] Open
Abstract
Natural minerals ('stone drugs') have been used in traditional Chinese medicines for over 2000 years, but there is potential for modern-day use of inorganic minerals to combat viral infections, antimicrobial resistance, and for other areas in need of new therapies and diagnostic aids. Metal and mineral surfaces on scales from milli-to nanometres, either natural or synthetic, are patterned or can be modified with hydrophilic/hydrophobic and ionic/covalent target-recognition sites. They introduce new strategies for medical applications. Such surfaces have novel properties compared to single metal centres. Moreover, 3D mineral particles (including hybrid organo-minerals) can have reactive cavities, and some minerals have dynamic movement of metal ions, anions, and other molecules within their structures. Minerals have a unique ability to interact with viruses, microbes and macro-biomolecules through multipoint ionic and/or non-covalent contacts, with potential for novel applications in therapy and biotechnology. Investigations of mineral deposits in biology, with their often inherent heterogeneity and tendency to become chemically-modified on isolation, are highly challenging, but new methods for their study, including in intact tissues, hold promise for future advances.
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Affiliation(s)
- Oliver W L Carter
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
- MAS CDT, Senate House, University of Warwick Coventry CV4 7AL UK
| | - Yingjian Xu
- GoldenKeys High-Tech Materials Co., Ltd, Building B, Innovation & Entrepreneurship Park Guian New Area Guizhou Province 550025 China
| | - Peter J Sadler
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
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25
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Rivera-Perez C, Flores-Sánchez IA, Ojeda Ramírez de Areyano JJ, Rojas Posadas DI, Hernández-Saavedra NY. A shell matrix protein of Pinctada mazatlanica produces nacre platelets in vitro. Sci Rep 2020; 10:20201. [PMID: 33214608 PMCID: PMC7677314 DOI: 10.1038/s41598-020-77320-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 11/09/2020] [Indexed: 11/09/2022] Open
Abstract
AbstractNacre is the main component of the pearl oyster shells and it is synthesized by specialized soluble and insoluble shell matrix proteins. Insoluble proteins from the decalcification of the shell are the less studied proteins due to the technical problems to isolate them from the organic matrix. In this study, an insoluble shell matrix protein from Pinctada mazatlanica, pearlin (Pmaz-pearlin), was successfully cloned from the mantle tissue, and the native protein isolated from the shell was functionally characterized. The full coding sequence of Pmaz-pearlin mRNA consists of 423 base pairs, which encode to a 16.3 kDa pearlin. Analysis of the deduced amino acid sequence revealed that Pmaz-pearlin contained four acidic regions, an NG repeat domain, and Cys conserved residues, the latter potentially forms four disulfide bridges which might stabilize the protein structure. The isolated protein from the shell is a glycoprotein of ~ 16.74 kDa which can produce aragonite and calcite crystals in vitro. Our results show that Pmaz-pearlin is a well-conserved protein involved in nacre layer growth, which produces calcite crystals in the presence of CaCl2, aragonite crystal polymorphs with a hexagonal structure in the presence of MgCl2, and needle-like crystal structure polymorphs in the presence of CaCO3 The identity of the crystals was confirmed using RAMAN analyses.
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Shimizu K, Kintsu H, Awaji M, Matumoto T, Suzuki M. Evolution of Biomineralization Genes in the Prismatic Layer of the Pen Shell Atrina pectinata. J Mol Evol 2020; 88:742-758. [PMID: 33236260 DOI: 10.1007/s00239-020-09977-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/18/2020] [Indexed: 11/29/2022]
Abstract
Molluscan shells are composed of calcium carbonates, with small amounts of extracellular matrices secreted from mantle epithelial cells. Many types of shell matrix proteins (SMPs) have been identified from molluscan shells or mantle cells. The pen shell Atrina pectinata (Pinnidae) has two different shell microstructures, the nacreous and prismatic layers. Nacreous and prismatic layer-specific matrix proteins have been reported in Pteriidae bivalves, but remain unclear in Pinnidae. We performed transcriptome analysis using the mantle cells of A. pectinata to screen the candidate transcripts involved in its prismatic layer formation. We found Asprich and nine highly conserved prismatic layer-specific SMPs encoding transcript in P. fucata, P. margaritifera, and P. maxima (Tyrosinase, Chitinase, EGF-like proteins, Fibronectin, valine-rich proteins, and prismatic uncharacterized shell protein 2 [PUSP2]) using molecular phylogenetic analysis or multiple alignment. We confirmed these genes were expressed in the epithelial cells of the mantle edge (outer surface of the outer fold) and the mantle pallium. Phylogenetic character mapping of these SMPs was used to infer a possible evolutionary scenario of them in Pteriomorphia. EGF-like proteins, Fibronectin, and valine-rich proteins encoding genes each evolved in the linage leading to four Pteriomorphia (Mytilidae, Pinnidae, Ostreidae, and Pteriidae), PUSP2 evolved in the linage leading to three Pteriomorphia families (Pinnidae, Ostreidae, and Pteriidae), and chitinase was independently evolved as SMPs in Mytilidae and in other Pteriomorphia (Pinnidae, Ostreidae, and Pteriidae). Our results provide a new dataset for A. pectinata SMP annotation, and a basis for understanding the evolution of prismatic layer formation in bivalves.
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Affiliation(s)
- Keisuke Shimizu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Hiroyuki Kintsu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan.,Center for Health and Environmental Risk Research, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Masahiko Awaji
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 422-1 Nakatsuhama, Minami-Ise, Watarai, Mie, 516-0193, Japan
| | - Toshie Matumoto
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 422-1 Nakatsuhama, Minami-Ise, Watarai, Mie, 516-0193, Japan
| | - Michio Suzuki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan.
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Sleight VA, Antczak P, Falciani F, Clark MS. Computationally predicted gene regulatory networks in molluscan biomineralization identify extracellular matrix production and ion transportation pathways. Bioinformatics 2020; 36:1326-1332. [PMID: 31617561 PMCID: PMC7703775 DOI: 10.1093/bioinformatics/btz754] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 09/07/2019] [Accepted: 10/07/2019] [Indexed: 01/09/2023] Open
Abstract
MOTIVATION The molecular processes regulating molluscan shell production remain relatively uncharacterized, despite the clear evolutionary and societal importance of biomineralization. RESULTS Here we built the first computationally predicted gene regulatory network (GRN) for molluscan biomineralization using Antarctic clam (Laternula elliptica) mantle gene expression data produced over an age-categorized shell damage-repair time-course. We used previously published in vivo in situ hybridization expression data to ground truth gene interactions predicted by the GRN and show that candidate biomineralization genes from different shell layers, and hence microstructures, were connected in unique modules. We characterized two biomineralization modules of the GRN and hypothesize that one module is responsible for translating the extracellular proteins required for growing, repairing or remodelling the nacreous shell layer, whereas the second module orchestrates the transport of both ions and proteins to the shell secretion site, which are required during normal shell growth, and repair. Our findings demonstrate that unbiased computational methods are particularly valuable for studying fundamental biological processes and gene interactions in non-model species where rich sources of gene expression data exist, but annotation rates are poor and the ability to carry out true functional tests are still lacking. AVAILABILITY AND IMPLEMENTATION The raw RNA-Seq data is freely available for download from NCBI SRA (Accession: PRJNA398984), the assembled and annotated transcriptome can be viewed and downloaded from molluscDB (ensembl.molluscdb.org) and in addition, the assembled transcripts, reconstructed GRN, modules and detailed annotations are all available as Supplementary Files. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Victoria A Sleight
- Department of Zoology, University of Cambridge, Cambridge, UK.,Biodiversity, Evolution and Adaptation Team, British Antarctic Survey, Cambridge, UK
| | - Philipp Antczak
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Francesco Falciani
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Melody S Clark
- Biodiversity, Evolution and Adaptation Team, British Antarctic Survey, Cambridge, UK
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28
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Klein AH, Ballard KR, Storey KB, Motti CA, Zhao M, Cummins SF. Multi-omics investigations within the Phylum Mollusca, Class Gastropoda: from ecological application to breakthrough phylogenomic studies. Brief Funct Genomics 2020; 18:377-394. [PMID: 31609407 DOI: 10.1093/bfgp/elz017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/06/2019] [Accepted: 07/15/2019] [Indexed: 12/22/2022] Open
Abstract
Gastropods are the largest and most diverse class of mollusc and include species that are well studied within the areas of taxonomy, aquaculture, biomineralization, ecology, microbiome and health. Gastropod research has been expanding since the mid-2000s, largely due to large-scale data integration from next-generation sequencing and mass spectrometry in which transcripts, proteins and metabolites can be readily explored systematically. Correspondingly, the huge data added a great deal of complexity for data organization, visualization and interpretation. Here, we reviewed the recent advances involving gastropod omics ('gastropodomics') research from hundreds of publications and online genomics databases. By summarizing the current publicly available data, we present an insight for the design of useful data integrating tools and strategies for comparative omics studies in the future. Additionally, we discuss the future of omics applications in aquaculture, natural pharmaceutical biodiscovery and pest management, as well as to monitor the impact of environmental stressors.
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Affiliation(s)
- Anne H Klein
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Kaylene R Ballard
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Kenneth B Storey
- Institute of Biochemistry & Department of Biology, Carleton University, Ottawa, ON, Canada K1S 5B6
| | - Cherie A Motti
- Australian Institute of Marine Science (AIMS), Cape Ferguson, Townsville Queensland 4810, Australia
| | - Min Zhao
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Scott F Cummins
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
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29
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Proteomic investigation of the blue mussel larval shell organic matrix. J Struct Biol 2019; 208:107385. [DOI: 10.1016/j.jsb.2019.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/04/2019] [Accepted: 09/06/2019] [Indexed: 11/22/2022]
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30
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Zhang YX, Wang JX, Wang XW. First identification and characterization of a triple WAP domain containing protein in Procambarus clarkii provides new insights into the classification and evolution of WAP proteins in crustacean. FISH & SHELLFISH IMMUNOLOGY 2019; 94:592-598. [PMID: 31518688 DOI: 10.1016/j.fsi.2019.09.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/20/2019] [Accepted: 09/10/2019] [Indexed: 06/10/2023]
Abstract
Whey acidic protein domain (WAPD) is a usual motif in crustaceans, and is found mainly in the immune-related proteins. In the present study, a protein containing three tandem WAPDs was identified in red swamp crayfish Procambarus clarkii and designated as PcTWD. This is the first report of a protein of such domain architecture in crustaceans. Introducing the WAPDs of PcTWD into phylogenetic analysis led to the classification of crustacean WAP proteins into classical crustins and proteins containing solely WAPDs. PcTWD was widely expressed in multiple tissues, including hemocytes, gills, hepatopancreas, heart, stomach and intestine. Its expression could be significantly induced by Staphylococcus aureus or Aeromonas hydrophila challenge. Knockdown PcTWD expression by RNAi suppressed host resistance against A. hydrophila, while exogenous recombinant PcTWD could enhance the host immunity. The three WAPDs showed a labor division. The first two domains were responsible for the protease inhibitory activity, and the third domain contributed to the antimicrobial activity. Thus PcTWD was found as an important protein in crayfish antibacterial immunity.
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Affiliation(s)
- Yu-Xuan Zhang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Qingdao, 266237, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Jin-Xing Wang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Qingdao, 266237, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Xian-Wei Wang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Qingdao, 266237, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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31
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Crystal growth kinetics as an architectural constraint on the evolution of molluscan shells. Proc Natl Acad Sci U S A 2019; 116:20388-20397. [PMID: 31551265 PMCID: PMC6789867 DOI: 10.1073/pnas.1907229116] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Using notions from classic materials science, we expand our understanding of the macroscopic morphospace of possible molluscan shell shapes to the level of possible ultrastructures that comprise them. This provides us with a unique opportunity to explore this morphospace using well-developed analytical, theoretical, and numerical tools and to test the effects of a discrete number of parameters on shell biomineralization. The physical model presented here sheds a new light on the evolutionary aspect of molluscan shell ultrastructural fabrication and suggests that the repeated “discovery” of some mineral morphologies partially reflects a series of architectural constraints provided by biomineral growth kinetics. Molluscan shells are a classic model system to study formation–structure–function relationships in biological materials and the process of biomineralized tissue morphogenesis. Typically, each shell consists of a number of highly mineralized ultrastructures, each characterized by a specific 3D mineral–organic architecture. Surprisingly, in some cases, despite the lack of a mutual biochemical toolkit for biomineralization or evidence of homology, shells from different independently evolved species contain similar ultrastructural motifs. In the present study, using a recently developed physical framework, which is based on an analogy to the process of directional solidification and simulated by phase-field modeling, we compare the process of ultrastructural morphogenesis of shells from 3 major molluscan classes: A bivalve Unio pictorum, a cephalopod Nautilus pompilius, and a gastropod Haliotis asinina. We demonstrate that the fabrication of these tissues is guided by the organisms by regulating the chemical and physical boundary conditions that control the growth kinetics of the mineral phase. This biomineralization concept is postulated to act as an architectural constraint on the evolution of molluscan shells by defining a morphospace of possible shell ultrastructures that is bounded by the thermodynamics and kinetics of crystal growth.
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32
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Liao Z, Jiang YT, Sun Q, Fan MH, Wang JX, Liang HY. Microstructure and in-depth proteomic analysis of Perna viridis shell. PLoS One 2019; 14:e0219699. [PMID: 31323046 PMCID: PMC6641155 DOI: 10.1371/journal.pone.0219699] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 06/28/2019] [Indexed: 12/20/2022] Open
Abstract
For understanding the structural characteristics and the proteome of Perna shell, the microstructure, polymorph, and protein composition of the adult Perna viridis shell were investigated. The P. viridis shell have two distinct mineral layers, myostracum and nacre, with the same calcium carbonate polymorph of aragonite, determined by scanning electron microscope, Fourier transform infrared spectroscopy, and x-ray crystalline diffraction. Using Illumina sequencing, the mantle transcriptome of P. viridis was investigated and a total of 69,859 unigenes was generated. Using a combined proteomic/transcriptomic approach, a total of 378 shell proteins from P. viridis shell were identified, in which, 132 shell proteins identified with more than two matched unique peptides. Of the 132 shell proteins, 69 are exclusive to the nacre, 12 to the myostracum, and 51 are shared by both. The Myosin-tail domain containing proteins, Filament-like proteins, and Chitin-binding domain containing proteins represent the most abundant molecules. In addition, the shell matrix proteins (SMPs) containing biomineralization-related domains, such as Kunitz, A2M, WAP, EF-hand, PDZ, VWA, Collagen domain, and low complexity regions with abundant certain amino acids, were also identified from P. viridis shell. Collagenase and chitinase degradation can significantly change the morphology of the shell, indicating the important roles of collagen and chitin in the shell formation and the muscle-shell attachment. Our results present for the first time the proteome of P. viridis shell and increase the knowledge of SMPs in this genus.
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Affiliation(s)
- Zhi Liao
- Laboratory of Marine Biological Source and Molecular Engineering, College of Marine Science, Zhejiang Ocean University, Zhoushan, Zhejiang, P.R. China
| | - Yu-ting Jiang
- Laboratory of Marine Biological Source and Molecular Engineering, College of Marine Science, Zhejiang Ocean University, Zhoushan, Zhejiang, P.R. China
| | - Qi Sun
- Laboratory of Marine Biological Source and Molecular Engineering, College of Marine Science, Zhejiang Ocean University, Zhoushan, Zhejiang, P.R. China
| | - Mei-hua Fan
- Laboratory of Marine Biological Source and Molecular Engineering, College of Marine Science, Zhejiang Ocean University, Zhoushan, Zhejiang, P.R. China
| | - Jian-xin Wang
- Laboratory of Marine Biological Source and Molecular Engineering, College of Marine Science, Zhejiang Ocean University, Zhoushan, Zhejiang, P.R. China
| | - Hai-ying Liang
- Fisheries College, Guangdong Ocean University, Zhanjiang, Guangdong, P.R. China
- * E-mail:
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33
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Jin C, Liu XJ, Li JL. A Kunitz proteinase inhibitor (HcKuPI) participated in antimicrobial process during pearl sac formation and induced the overgrowth of calcium carbonate in Hyriopsis cumingii. FISH & SHELLFISH IMMUNOLOGY 2019; 89:437-447. [PMID: 30980916 DOI: 10.1016/j.fsi.2019.04.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/06/2019] [Accepted: 04/07/2019] [Indexed: 06/09/2023]
Abstract
Proteinase inhibitors with the ability to inhibit specific proteinases are usually closely connected with the immune system. Interestingly, proteinase inhibitors are also a common ingredient in the organic matrix of mollusk shells. However, the molecular mechanism that underlies the role of proteinase inhibitors in immune system and shell mineralization is poorly known. In this study, a Kunitz serine proteinase inhibitor (HcKuPI) was isolated from the mussel Hyriopsis cumingii. HcKuPI was specifically expressed in dorsal epithelial cells of the mantle pallium and HcKuPI dsRNA injection caused an irregular surface and disordered deposition on the aragonite tablets of the nacreous layer. These results indicated that HcKuPI plays a vital role in shell nacreous layer biomineralization. Moreover, the expression pattern of HcKuPI during LPS challenge and pearl formation indicated its involvement in the antimicrobial process during pearl sac formation and nacre tablets accumulation during pearl formation. In the in vitro calcium carbonate crystallization assay, the addition of GST-HcKuPI increased the precipitation rate of calcium carbonate and induced the crystal overgrowth of calcium carbonate. Taken together, these results indicate that HcKuPI is involved in antimicrobial process during pearl formation, and participates in calcium carbonate deposition acceleration and morphological regulation of the crystals during nacreous layer formation. These findings extend our knowledge of the role of proteinase inhibitors in immune system and shell biomineralization.
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Affiliation(s)
- Can Jin
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai, 201306, China
| | - Xiao-Jun Liu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.
| | - Jia-Le Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai, 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306, China.
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34
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Shimizu K, Kimura K, Isowa Y, Oshima K, Ishikawa M, Kagi H, Kito K, Hattori M, Chiba S, Endo K. Insights into the Evolution of Shells and Love Darts of Land Snails Revealed from Their Matrix Proteins. Genome Biol Evol 2019; 11:380-397. [PMID: 30388206 PMCID: PMC6368272 DOI: 10.1093/gbe/evy242] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2018] [Indexed: 12/14/2022] Open
Abstract
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.
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Affiliation(s)
- Keisuke Shimizu
- Department of Earth and Planetary Science, The University of Tokyo, Hongo, Japan
- College of Life and Environmental Sciences, University of Exeter, United Kingdom
| | - Kazuki Kimura
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
- Research Institute for Ulleungdo and Dokdo Islands, Kyungpook National University, Bukgu, Daegu, Korea
| | - Yukinobu Isowa
- Organization for the Strategic Coordination of Research and Intellectual Properties, Meiji University, Kawasaki, Kanagawa, Japan
| | - Kenshiro Oshima
- Center for Omics and Bioinformatics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Makiko Ishikawa
- Department of Earth and Planetary Science, The University of Tokyo, Hongo, Japan
- Faculty of Animal Health Technology, Yamazaki University of Animal Health Technology, Hachioji, Tokyo, Japan
| | - Hiroyuki Kagi
- Geochemical Research Center, Graduate School of Science, The University of Tokyo, Hongo, Japan
| | - Keiji Kito
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Masahira Hattori
- Center for Omics and Bioinformatics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
- Cooperative Major of Advanced Health Science, Graduate School of Advanced Science and Engineering, Waseda University, Japan
| | - Satoshi Chiba
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Kazuyoshi Endo
- Department of Earth and Planetary Science, The University of Tokyo, Hongo, Japan
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35
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McDougall C, Hammond MJ, Dailey SC, Somorjai IML, Cummins SF, Degnan BM. The evolution of ependymin-related proteins. BMC Evol Biol 2018; 18:182. [PMID: 30514200 PMCID: PMC6280359 DOI: 10.1186/s12862-018-1306-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 11/23/2018] [Indexed: 12/19/2022] Open
Abstract
Background Ependymins were originally defined as fish-specific secreted glycoproteins involved in central nervous system plasticity and memory formation. Subsequent research revealed that these proteins represent a fish-specific lineage of a larger ependymin-related protein family (EPDRs). EPDRs have now been identified in a number of bilaterian animals and have been implicated in diverse non-neural functions. The recent discoveries of putative EPDRs in unicellular holozoans and an expanded EPDR family with potential roles in conspecific communication in crown-of-thorns starfish suggest that the distribution and diversity of EPDRs is significantly broader than currently understood. Results We undertook a systematic survey to determine the distribution and evolution of EPDRs in eukaryotes. In addition to Bilateria, EPDR genes were identified in Cnidaria, Placozoa, Porifera, Choanoflagellatea, Filasterea, Apusozoa, Amoebozoa, Charophyta and Percolozoa, and tentatively in Cercozoa and the orphan group Malawimonadidae. EPDRs appear to be absent from prokaryotes and many eukaryote groups including ecdysozoans, fungi, stramenopiles, alveolates, haptistans and cryptistans. The EPDR family can be divided into two major clades and has undergone lineage-specific expansions in a number of metazoan lineages, including in poriferans, molluscs and cephalochordates. Variation in a core set of conserved residues in EPDRs reveals the presence of three distinct protein types; however, 3D modelling predicts overall protein structures to be similar. Conclusions Our results reveal an early eukaryotic origin of the EPDR gene family and a dynamic pattern of gene duplication and gene loss in animals. This research provides a phylogenetic framework for the analysis of the functional evolution of this gene family. Electronic supplementary material The online version of this article (10.1186/s12862-018-1306-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Carmel McDougall
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, Brisbane, Queensland, 4072, Australia.,Australian Rivers Institute, Griffith University, Nathan, Queensland, 4111, Australia
| | - Michael J Hammond
- GeneCology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia
| | - Simon C Dailey
- Gatty Marine Laboratory, Scottish Oceans Institute, University of St Andrews, St Andrews, KY16 8LB, UK.,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Ildiko M L Somorjai
- Gatty Marine Laboratory, Scottish Oceans Institute, University of St Andrews, St Andrews, KY16 8LB, UK.,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Scott F Cummins
- GeneCology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia
| | - Bernard M Degnan
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, Brisbane, Queensland, 4072, Australia.
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36
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Schoeppler V, Gránásy L, Reich E, Poulsen N, de Kloe R, Cook P, Rack A, Pusztai T, Zlotnikov I. Biomineralization as a Paradigm of Directional Solidification: A Physical Model for Molluscan Shell Ultrastructural Morphogenesis. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1803855. [PMID: 30239045 DOI: 10.1002/adma.201803855] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/15/2018] [Indexed: 05/12/2023]
Abstract
Molluscan shells are a model system to understand the fundamental principles of mineral formation by living organisms. The diversity of unconventional mineral morphologies and 3D mineral-organic architectures that comprise these tissues, in combination with their exceptional mechanical efficiency, offers a unique platform to study the formation-structure-function relationship in a biomineralized system. However, so far, morphogenesis of these ultrastructures is poorly understood. Here, a comprehensive physical model, based on the concept of directional solidification, is developed to describe molluscan shell biomineralization. The capacity of the model to define the forces and thermodynamic constraints that guide the morphogenesis of the entire shell construct-the prismatic and nacreous ultrastructures and their transitions-and govern the evolution of the constituent mineralized assemblies on the ultrastructural and nanostructural levels is demonstrated using the shell of the bivalve Unio pictorum. Thereby, explicit tools for novel bioinspired and biomimetic bottom-up materials design are provided.
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Affiliation(s)
- Vanessa Schoeppler
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, 01307, Germany
| | - László Gránásy
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Budapest, 1121, Hungary
| | - Elke Reich
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, 01307, Germany
| | - Nicole Poulsen
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, 01307, Germany
| | | | - Phil Cook
- ESRF - The European Synchrotron, Grenoble, 38043, France
| | - Alexander Rack
- ESRF - The European Synchrotron, Grenoble, 38043, France
| | - Tamás Pusztai
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Budapest, 1121, Hungary
| | - Igor Zlotnikov
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, 01307, Germany
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Van Wormhoudt A, del Río Portilla MÁ, Auzoux-Bordenave S. Gene structure and domain architecture in the biomineralizing protein Lustrin A from the abalone Haliotis rufescens. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Mann K, Cerveau N, Gummich M, Fritz M, Mann M, Jackson DJ. In-depth proteomic analyses of Haliotis laevigata (greenlip abalone) nacre and prismatic organic shell matrix. Proteome Sci 2018; 16:11. [PMID: 29983641 PMCID: PMC6003135 DOI: 10.1186/s12953-018-0139-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/25/2018] [Indexed: 01/12/2023] Open
Abstract
Background The shells of various Haliotis species have served as models of invertebrate biomineralization and physical shell properties for more than 20 years. A focus of this research has been the nacreous inner layer of the shell with its conspicuous arrangement of aragonite platelets, resembling in cross-section a brick-and-mortar wall. In comparison, the outer, less stable, calcitic prismatic layer has received much less attention. One of the first molluscan shell proteins to be characterized at the molecular level was Lustrin A, a component of the nacreous organic matrix of Haliotis rufescens. This was soon followed by the C-type lectin perlucin and the growth factor-binding perlustrin, both isolated from H. laevigata nacre, and the crystal growth-modulating AP7 and AP24, isolated from H. rufescens nacre. Mass spectrometry-based proteomics was subsequently applied to to Haliotis biomineralization research with the analysis of the H. asinina shell matrix and yielded 14 different shell-associated proteins. That study was the most comprehensive for a Haliotis species to date. Methods The shell proteomes of nacre and prismatic layer of the marine gastropod Haliotis laevigata were analyzed combining mass spectrometry-based proteomics and next generation sequencing. Results We identified 297 proteins from the nacreous shell layer and 350 proteins from the prismatic shell layer from the green lip abalone H. laevigata. Considering the overlap between the two sets we identified a total of 448 proteins. Fifty-one nacre proteins and 43 prismatic layer proteins were defined as major proteins based on their abundance at more than 0.2% of the total. The remaining proteins occurred at low abundance and may not play any significant role in shell fabrication. The overlap of major proteins between the two shell layers was 17, amounting to a total of 77 major proteins. Conclusions The H. laevigata shell proteome shares moderate sequence similarity at the protein level with other gastropod, bivalve and more distantly related invertebrate biomineralising proteomes. Features conserved in H. laevigata and other molluscan shell proteomes include short repetitive sequences of low complexity predicted to lack intrinsic three-dimensional structure, and domains such as tyrosinase, chitin-binding, and carbonic anhydrase. This catalogue of H. laevigata shell proteins represents the most comprehensive for a haliotid and should support future efforts to elucidate the molecular mechanisms of shell assembly. Electronic supplementary material The online version of this article (10.1186/s12953-018-0139-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Karlheinz Mann
- 1Abteilung Proteomics und Signaltransduktion, Max-Planck-Institut für Biochemie, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Nicolas Cerveau
- 2Department of Geobiology, Georg-August University of Göttingen, Goldschmidstr. 3, 37077 Göttingen, Germany
| | - Meike Gummich
- 3Universität Bremen, Institut für Biophysik, Otto Hahn Allee NW1, D-28334 Bremen, Germany
| | - Monika Fritz
- 3Universität Bremen, Institut für Biophysik, Otto Hahn Allee NW1, D-28334 Bremen, Germany
| | - Matthias Mann
- 1Abteilung Proteomics und Signaltransduktion, Max-Planck-Institut für Biochemie, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Daniel J Jackson
- 2Department of Geobiology, Georg-August University of Göttingen, Goldschmidstr. 3, 37077 Göttingen, Germany
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Herlitze I, Marie B, Marin F, Jackson DJ. Molecular modularity and asymmetry of the molluscan mantle revealed by a gene expression atlas. Gigascience 2018; 7:4997018. [PMID: 29788257 PMCID: PMC6007483 DOI: 10.1093/gigascience/giy056] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 05/09/2018] [Indexed: 12/31/2022] Open
Abstract
Background Conchiferan molluscs construct a biocalcified shell that likely supported much of their evolutionary success. However, beyond broad proteomic and transcriptomic surveys of molluscan shells and the shell-forming mantle tissue, little is known of the spatial and ontogenetic regulation of shell fabrication. In addition, most efforts have been focused on species that deposit nacre, which is at odds with the majority of conchiferan species that fabricate shells using a crossed-lamellar microstructure, sensu lato. Results By combining proteomic and transcriptomic sequencing with in situ hybridization we have identified a suite of gene products associated with the production of the crossed-lamellar shell in Lymnaea stagnalis. With this spatial expression data we are able to generate novel hypotheses of how the adult mantle tissue coordinates the deposition of the calcified shell. These hypotheses include functional roles for unusual and otherwise difficult-to-study proteins such as those containing repetitive low-complexity domains. The spatial expression readouts of shell-forming genes also reveal cryptic patterns of asymmetry and modularity in the shell-forming cells of larvae and adult mantle tissue. Conclusions This molecular modularity of the shell-forming mantle tissue hints at intimate associations between structure, function, and evolvability and may provide an elegant explanation for the evolutionary success of the second largest phylum among the Metazoa.
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Affiliation(s)
- Ines Herlitze
- Department of Geobiology, Georg-August University of Göttingen, Goldschmidtstrasse 3, 37077 Göttingen, Germany
| | - Benjamin Marie
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Département Aviv, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 39, 12 Rue Buffon, 75005 Paris, France
| | - Frédéric Marin
- UMR CNRS 6282 Biogéosciences, Université de Bourgogne - Franche-Comté, 6 Boulevard Gabriel, 21000 Dijon, France
| | - Daniel J Jackson
- Department of Geobiology, Georg-August University of Göttingen, Goldschmidtstrasse 3, 37077 Göttingen, Germany
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Marie B, Arivalagan J, Mathéron L, Bolbach G, Berland S, Marie A, Marin F. Deep conservation of bivalve nacre proteins highlighted by shell matrix proteomics of the Unionoida Elliptio complanata and Villosa lienosa. J R Soc Interface 2017; 14:rsif.2016.0846. [PMID: 28123096 DOI: 10.1098/rsif.2016.0846] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/20/2016] [Indexed: 01/12/2023] Open
Abstract
The formation of the molluscan shell nacre is regulated to a large extent by a matrix of extracellular macromolecules that are secreted by the shell-forming tissue, the mantle. This so-called 'calcifying matrix' is a complex mixture of proteins, glycoproteins and polysaccharides that is assembled and occluded within the mineral phase during the calcification process. Better molecular-level characterization of the substances that regulate nacre formation is still required. Notable advances in expressed tag sequencing of freshwater mussels, such as Elliptio complanata and Villosa lienosa, provide a pre-requisite to further characterize bivalve nacre proteins by a proteomic approach. In this study, we have identified a total of 48 different proteins from the insoluble matrices of the nacre, 31 of which are common to both E. complanata and V. lienosa A few of these proteins, such as PIF, MSI60, CA, shematrin-like, Kunitz-like, LamG, chitin-binding-containing proteins, together with A-, D-, G-, M- and Q-rich proteins, appear to be analogues, if not true homologues, of proteins previously described from the pearl oyster or the edible mussel nacre matrices, thus forming a remarkable list of deeply conserved nacre proteins. This work constitutes a comprehensive nacre proteomic study of non-pteriomorphid bivalves that has enabled us to describe the molecular basis of a deeply conserved biomineralization toolkit among nacreous shell-bearing bivalves, with regard to proteins associated with other shell microstructures, with those of other mollusc classes (gastropods, cephalopods) and, finally, with other lophotrochozoans (brachiopods).
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Affiliation(s)
- Benjamin Marie
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Muséum National d'Histoire Naturelle, Sorbonne Universités, Paris, France
| | - Jaison Arivalagan
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Muséum National d'Histoire Naturelle, Sorbonne Universités, Paris, France
| | - Lucrèce Mathéron
- UMR 7203 CNRS/UPMC/ENS/INSERM Laboratoire des Biomolécules, Institut de Biologie Paris Seine, Université Pierre et Marie Curie, Sorbonne Universités, Paris, France
| | - Gérard Bolbach
- UMR 7203 CNRS/UPMC/ENS/INSERM Laboratoire des Biomolécules, Institut de Biologie Paris Seine, Université Pierre et Marie Curie, Sorbonne Universités, Paris, France
| | - Sophie Berland
- UMR 7208 CNRS/MNHN/UPMC/IRD Biologie des Organismes Aquatiques et Ecosystèmes, Muséum National d'Histoire Naturelle, Sorbonne Universités, Paris, France
| | - Arul Marie
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Muséum National d'Histoire Naturelle, Sorbonne Universités, Paris, France
| | - Frédéric Marin
- UMR 6282 CNRS/uB Biogéosciences, Université de Bourgogne Franche-Comté (UB-FC), Dijon, France
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Calvo-Iglesias J, Pérez-Estévez D, González-Fernández Á. MSP22.8 is a protease inhibitor-like protein involved in shell mineralization in the edible mussel Mytilus galloprovincialis. FEBS Open Bio 2017; 7:1539-1556. [PMID: 28979842 PMCID: PMC5623705 DOI: 10.1002/2211-5463.12286] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 08/01/2017] [Accepted: 08/02/2017] [Indexed: 01/01/2023] Open
Abstract
The mussel shell protein 22.8 (MSP22.8) is recognized by a monoclonal antibody (M22.8) directed against larvae of the mussel Mytilus galloprovincialis. After being secreted by cells of the mantle-edge epithelium into the extrapallial (EP) space (the gap between the mantle and the shell), the protein is detected in the extrapallial fluid (EPF) and EP hemocytes and finally becomes part of the shell matrix framework in adult specimens of M. galloprovincialis. In the work described here, we show how MSP22.8 is detected in EPF samples from different species of mussels (M. galloprovincialis, Mytilus edulis, and Xenostrobus securis), and also as a shell matrix protein in M. galloprovincialis, Mytilus chilensis, and Perna canaliculus. A multistep purification strategy was employed to isolate the protein from the EPF, which was then analyzed by mass spectrometry in order to identify it. The results indicate that MSP22.8 is a serpin-like protein that has great similarity with the protease inhibitor-like protein-B1, reported previously for Mytilus coruscus. We suggest that MSP22.8 is part of a system offering protection from proteolysis during biomineralization and is also part of the innate immune system in mussels.
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Affiliation(s)
- Juan Calvo-Iglesias
- Immunology Biomedical Research Center (CINBIO) Centro Singular de investigación de Galicia Institute of Biomedical Research of Vigo (IBIV) University of Vigo Pontevedra Spain
| | | | - África González-Fernández
- Immunology Biomedical Research Center (CINBIO) Centro Singular de investigación de Galicia Institute of Biomedical Research of Vigo (IBIV) University of Vigo Pontevedra Spain
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Gleason FH, Gadd GM, Pitt JI, Larkum AWD. The roles of endolithic fungi in bioerosion and disease in marine ecosystems. I. General concepts. Mycology 2017; 8:205-215. [PMID: 30123641 PMCID: PMC6059151 DOI: 10.1080/21501203.2017.1352049] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/03/2017] [Indexed: 01/30/2023] Open
Abstract
Endolithic true fungi and fungus-like microorganisms penetrate calcareous substrates formed by living organisms, cause significant bioerosion and are involved in diseases of many host animals in marine ecosystems. A theoretical interactive model for the ecology of reef-building corals is proposed in this review. This model includes five principle partners that exist in a dynamic equilibrium: polyps of a colonial coelenterate, endosymbiotic zooxanthellae, endolithic algae (that penetrate coral skeletons), endolithic fungi (that attack the endolithic algae, the zooxanthellae and the polyps) and prokaryotic and eukaryotic microorganisms (which live in the coral mucus). Endolithic fungi and fungus-like boring microorganisms are important components of the marine calcium carbonate cycle because they actively contribute to the biodegradation of shells of animals composed of calcium carbonate and calcareous geological substrates.
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Affiliation(s)
- Frank H. Gleason
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Geoffrey M Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, Scotland
| | - John I Pitt
- Food, Safety and Quality, CSIRO, Ryde, NSW, Australia
| | - Anthony W. D Larkum
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
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Feng D, Li Q, Yu H, Kong L, Du S. Identification of conserved proteins from diverse shell matrix proteome in Crassostrea gigas: characterization of genetic bases regulating shell formation. Sci Rep 2017; 7:45754. [PMID: 28374770 PMCID: PMC5379566 DOI: 10.1038/srep45754] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 03/06/2017] [Indexed: 12/21/2022] Open
Abstract
The calcifying shell is an excellent model for studying biomineralization and evolution. However, the molecular mechanisms of shell formation are only beginning to be elucidated in Mollusca. It is known that shell matrix proteins (SMPs) play important roles in shell formation. With increasing data of shell matrix proteomes from various species, we carried out a BLASTp bioinformatics analysis using the shell matrix proteome from Crassostrea gigas against 443 SMPs from nine other species. The highly conserved tyrosinase and chitin related proteins were identified in bivalve. In addition, the relatively conserved proteins containing domains of carbonic anhydrase, Sushi, Von Willebrand factor type A, and chitin binding, were identified from all the ten species. Moreover, 25 genes encoding SMPs were annotated and characterized that are involved in CaCO3 crystallization and represent chitin related or ECM related proteins. Together, data from these analyses provide new knowledge underlying the molecular mechanism of shell formation in C.gigas, supporting a refined shell formation model including chitin and ECM-related proteins.
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Affiliation(s)
- Dandan Feng
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Shaojun Du
- Institute of Marine and Environmental Technology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, United States
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Aguilera F, McDougall C, Degnan BM. Co-Option and De Novo Gene Evolution Underlie Molluscan Shell Diversity. Mol Biol Evol 2017; 34:779-792. [PMID: 28053006 PMCID: PMC5400390 DOI: 10.1093/molbev/msw294] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Molluscs fabricate shells of incredible diversity and complexity by localized secretions from the dorsal epithelium of the mantle. Although distantly related molluscs express remarkably different secreted gene products, it remains unclear if the evolution of shell structure and pattern is underpinned by the differential co-option of conserved genes or the integration of lineage-specific genes into the mantle regulatory program. To address this, we compare the mantle transcriptomes of 11 bivalves and gastropods of varying relatedness. We find that each species, including four Pinctada (pearl oyster) species that diverged within the last 20 Ma, expresses a unique mantle secretome. Lineage- or species-specific genes comprise a large proportion of each species' mantle secretome. A majority of these secreted proteins have unique domain architectures that include repetitive, low complexity domains (RLCDs), which evolve rapidly, and have a proclivity to expand, contract and rearrange in the genome. There are also a large number of secretome genes expressed in the mantle that arose before the origin of gastropods and bivalves. Each species expresses a unique set of these more ancient genes consistent with their independent co-option into these mantle gene regulatory networks. From this analysis, we infer lineage-specific secretomes underlie shell diversity, and include both rapidly evolving RLCD-containing proteins, and the continual recruitment and loss of both ancient and recently evolved genes into the periphery of the regulatory network controlling gene expression in the mantle epithelium.
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Affiliation(s)
- Felipe Aguilera
- Centre for Marine Sciences, School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Carmel McDougall
- Centre for Marine Sciences, School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Bernard M. Degnan
- Centre for Marine Sciences, School of Biological Sciences, The University of Queensland, Brisbane, Australia
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45
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First proteomic analyses of the dorsal and ventral parts of the Sepia officinalis cuttlebone. J Proteomics 2017; 150:63-73. [DOI: 10.1016/j.jprot.2016.08.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 08/19/2016] [Accepted: 08/23/2016] [Indexed: 12/12/2022]
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Arivalagan J, Yarra T, Marie B, Sleight VA, Duvernois-Berthet E, Clark MS, Marie A, Berland S. Insights from the Shell Proteome: Biomineralization to Adaptation. Mol Biol Evol 2017; 34:66-77. [PMID: 27744410 PMCID: PMC5854119 DOI: 10.1093/molbev/msw219] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Bivalves have evolved a range of complex shell forming mechanisms that are reflected by their incredible diversity in shell mineralogy and microstructures. A suite of proteins exported to the shell matrix space plays a significant role in controlling these features, in addition to underpinning some of the physical properties of the shell itself. Although, there is a general consensus that a minimum basic protein tool kit is required for shell construction, to date, this remains undefined. In this study, the shell matrix proteins (SMPs) of four highly divergent bivalves (The Pacific oyster, Crassostrea gigas; the blue mussel, Mytilus edulis; the clam, Mya truncata, and the king scallop, Pecten maximus) were analyzed in an identical fashion using proteomics pipeline. This enabled us to identify the critical elements of a "basic tool kit" for calcification processes, which were conserved across the taxa irrespective of the shell morphology and arrangement of the crystal surfaces. In addition, protein domains controlling the crystal layers specific to aragonite and calcite were also identified. Intriguingly, a significant number of the identified SMPs contained domains related to immune functions. These were often are unique to each species implying their involvement not only in immunity, but also environmental adaptation. This suggests that the SMPs are selectively exported in a complex mix to endow the shell with both mechanical protection and biochemical defense.
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Affiliation(s)
- Jaison Arivalagan
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Sorbonne Universités, Muséum national d'Histoire naturelle, Paris, France
- UMR 7208 CNRS/MNHN/UPMC/IRD Biologie des Organismes Aquatiques et Ecosystèmes, Sorbonne Universités, Muséum national d'Histoire naturelle, Paris, France
| | - Tejaswi Yarra
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, United Kingdom
- University of Edinburgh, Institute of Evolutionary Biology, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, United Kingdom
| | - Benjamin Marie
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Sorbonne Universités, Muséum national d'Histoire naturelle, Paris, France
| | - Victoria A Sleight
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, United Kingdom
| | - Evelyne Duvernois-Berthet
- UMR 7221 CNRS/MNHN Evolution des Régulations Endocriniennes, Sorbonne Universités, Muséum national d'Histoire naturelle, Paris, France
| | - Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, United Kingdom
| | - Arul Marie
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Sorbonne Universités, Muséum national d'Histoire naturelle, Paris, France
| | - Sophie Berland
- UMR 7208 CNRS/MNHN/UPMC/IRD Biologie des Organismes Aquatiques et Ecosystèmes, Sorbonne Universités, Muséum national d'Histoire naturelle, Paris, France
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Rao A, Cölfen H. Mineralization and non-ideality: on nature's foundry. Biophys Rev 2016; 8:309-329. [PMID: 28510024 DOI: 10.1007/s12551-016-0228-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 09/30/2016] [Indexed: 10/20/2022] Open
Abstract
Understanding how ions, ion-clusters and particles behave in non-ideal environments is a fundamental question concerning planetary to atomic scales. For biomineralization phenomena wherein diverse inorganic and organic ingredients are present in biological media, attributing biomaterial composition and structure to the chemistry of singular additives may not provide a holistic view of the underlying mechanisms. Therefore, in this review, we specifically address the consequences of physico-chemical non-ideality on mineral formation. Influences of different forms of non-ideality such as macromolecular crowding, confinement and liquid-like organic phases on mineral nucleation and crystallization in biological environments are presented. Novel prospects for the additive-controlled nucleation and crystallization are accessible from this biophysical view. In this manner, we show that non-ideal conditions significantly affect the form, structure and composition of biogenic and biomimetic minerals.
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Affiliation(s)
- Ashit Rao
- Freiburg Institute for Advanced Studies, Albert Ludwigs University of Freiburg, 79104, Freiburg im Breisgau, Germany.
| | - Helmut Cölfen
- Physical Chemistry, Department of Chemistry, University of Konstanz, D-78457, Konstanz, Germany.
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48
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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]
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49
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The importance of evo-devo to an integrated understanding of molluscan biomineralisation. J Struct Biol 2016; 196:67-74. [DOI: 10.1016/j.jsb.2016.01.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/10/2016] [Accepted: 01/11/2016] [Indexed: 01/05/2023]
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50
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Bal N, Kumar A, Du J, Nugegoda D. Prednisolone impairs embryonic and posthatching development and shell formation of the freshwater snail, Physa acuta. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2016; 35:2339-2348. [PMID: 26887568 DOI: 10.1002/etc.3401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 09/04/2015] [Accepted: 02/12/2016] [Indexed: 06/05/2023]
Abstract
The aim of the present study was to investigate the lethal and sublethal effects of prednisolone exposure on the embryonic and posthatching stage of the freshwater snail, Physa acuta. The egg masses were exposed for 14 d to prednisolone concentrations ranging from 15.6 μg/L to 1000 μg/L. Treatment with prednisolone at 125 μg/L to 1000 μg/L resulted in significant decline in growth, survival, and heart rate, as well as notable abnormalities in embryonic development. Premature embryonic hatching was observed at lower concentrations of 31.25 μg/L and 62.5 μg/L, whereas delayed hatching was seen at concentrations from 125 μg/L to 1000 μg/L. To assess impacts of prednisolone exposure on the hatched juveniles, the drug exposure was extended for another 28 d. Impairment of shell development was noted in juveniles exposed to concentrations from 62.5 μg/L to 1000 μg/L at the end of 42 d, which resulted in thin and fragile shells. The thickness of shells in snails exposed to 1000 μg/L was significantly lower in comparison to those in the 15.6-μg/L and control treatments. In addition, lower calcium concentration in shells of the exposed juvenile snails at treatments of 62.5 μg/L to 1000 μg/L consequently reduced their growth. The present study confirms that continuous exposure to prednisolone can result in deleterious effects on calcium deposition, resulting in shell thinning in the freshwater snail P. acuta. Environ Toxicol Chem 2016;35:2339-2348. © 2016 SETAC.
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Affiliation(s)
- Navdeep Bal
- RMIT University, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation Land and Water, Glen Osmond, South Australia, Australia
| | - Anu Kumar
- Commonwealth Scientific and Industrial Research Organisation Land and Water, Glen Osmond, South Australia, Australia
| | - Jun Du
- Commonwealth Scientific and Industrial Research Organisation Land and Water, Glen Osmond, South Australia, Australia
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