@article {7164, title = {Deciphering mollusc shell production: the roles of genetic mechanisms through to ecology, aquaculture and biomimetics.}, journal = {Biol Rev Camb Philos Soc}, year = {2020}, month = {2020 Jul 31}, abstract = {

Most molluscs possess shells, constructed from a vast array of microstructures and architectures. The fully formed shell is composed of calcite or aragonite. These CaCO crystals form complex biocomposites with proteins, which although typically less than 5\% of total shell mass, play significant roles in determining shell microstructure. Despite much research effort, large knowledge gaps remain in how molluscs construct and maintain their shells, and how they produce such a great diversity of forms. Here we synthesize results on how shell shape, microstructure, composition and organic content vary among, and within, species in response to numerous biotic and abiotic factors. At the local level, temperature, food supply and predation cues significantly affect shell morphology, whilst salinity has a much stronger influence across latitudes. Moreover, we emphasize how advances in genomic technologies [e.g. restriction site-associated DNA sequencing (RAD-Seq) and epigenetics] allow detailed examinations of whether morphological changes result from phenotypic plasticity or genetic adaptation, or a combination of these. RAD-Seq has already identified single nucleotide polymorphisms associated with temperature and aquaculture practices, whilst epigenetic processes have been shown significantly to modify shell construction to local conditions in, for example, Antarctica and New Zealand. We also synthesize results on the costs of shell construction and explore how these affect energetic trade-offs in animal metabolism. The cellular costs are still debated, with CaCO precipitation estimates ranging from 1-2 J/mg to 17-55 J/mg depending on experimental and environmental conditions. However, organic components are more expensive (~29 J/mg) and recent data indicate transmembrane calcium ion transporters can involve considerable costs. This review emphasizes the role that molecular analyses have played in demonstrating multiple evolutionary origins of biomineralization genes. Although these are characterized by lineage-specific proteins and unique combinations of co-opted genes, a small set of protein domains have been identified as a conserved biomineralization tool box. We further highlight the use of sequence data sets in providing candidate genes for in situ localization and protein function studies. The former has elucidated gene expression modularity in mantle tissue, improving understanding of the diversity of shell morphology synthesis. RNA interference (RNAi) and clustered regularly interspersed short palindromic repeats - CRISPR-associated protein 9 (CRISPR-Cas9) experiments have provided proof of concept for use in the functional investigation of mollusc gene sequences, showing for example that Pif (aragonite-binding) protein plays a significant role in structured nacre crystal growth and that the Lsdia1 gene sets shell chirality in Lymnaea stagnalis. Much research has focused on the impacts of ocean acidification on molluscs. Initial studies were predominantly pessimistic for future molluscan biodiversity. However, more sophisticated experiments incorporating selective breeding and multiple generations are identifying subtle effects and that variability within mollusc genomes has potential for adaption to future conditions. Furthermore, we highlight recent historical studies based on museum collections that demonstrate a greater resilience of molluscs to climate change compared with experimental data. The future of mollusc research lies not solely with ecological investigations into biodiversity, and this review synthesizes knowledge across disciplines to understand biomineralization. It spans research ranging from evolution and development, through predictions of biodiversity prospects and future-proofing of aquaculture to identifying new biomimetic opportunities and societal benefits from recycling shell products.

}, issn = {1469-185X}, doi = {10.1111/brv.12640}, author = {Clark, Melody S and Peck, Lloyd S and Arivalagan, Jaison and Backeljau, Thierry and Berland, Sophie and Cardoso, Joao C R and Caurcel, Carlos and Chapelle, Gauthier and De Noia, Michele and Dupont, Sam and Gharbi, Karim and Hoffman, Joseph I and Last, Kim S and Marie, Arul and Melzner, Frank and Michalek, Kati and Morris, James and Power, Deborah M and Ramesh, Kirti and Sanders, Trystan and Sillanp{\"a}{\"a}, Kirsikka and Sleight, Victoria A and Stewart-Sinclair, Phoebe J and Sundell, Kristina and Telesca, Luca and Vendrami, David L J and Ventura, Alexander and Wilding, Thomas A and Yarra, Tejaswi and Harper, Elizabeth M} } @article {8124, title = {Deciphering shell proteome within different Baltic populations of mytilid mussels illustrates important local variability and potential consequences in the context of changing marine conditions}, journal = {Science of The Total Environment}, volume = {745}, year = {2020}, month = {Jan-11-2020}, pages = {140878}, issn = {00489697}, doi = {10.1016/j.scitotenv.2020.140878}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0048969720344077}, author = {Arivalagan, Jaison and Marie, Benjamin and Chiappetta, Giovanni and Vinh, Jo{\"e}lle and Gallet, Xavier and Lebon, Matthieu and M{\textquoteright}Zoudi, Saloua and Dubois, Philippe and Berland, Sophie and Marie, Arul} } @article {4728, title = {Deep conservation of bivalve nacre proteins highlighted by shell matrix proteomics of the Unionoida Elliptio complanata and Villosa lienosa}, journal = {Journal of The Royal Society Interface}, volume = {14}, year = {2017}, 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 {\textquoteleft}calcifying matrix{\textquoteright} 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).

}, issn = {1742-5689}, doi = {10.1098/rsif.2016.0846}, url = {http://rsif.royalsocietypublishing.org/content/14/126/20160846}, author = {Marie, Benjamin and Arivalagan, Jaison and Math{\'e}ron, Lucr{\`e}ce and Bolbach, G{\'e}rard and Berland, Sophie and Marie, Arul and Marin, Fr{\'e}d{\'e}ric} } @article {4526, title = {First proteomic analyses of the dorsal and ventral parts of the Sepia officinalis cuttlebone.}, journal = {J Proteomics}, volume = {150}, year = {2017}, month = {2016 Aug 26}, pages = {63-73}, abstract = {

Protein compounds constituting mollusk shells are known for their major roles in the biomineralization processes. These last years, a great diversity of shell proteins have been described in bivalves and gastropods allowing a better understanding of the calcification control by organic compounds and given promising applications in biotechnology. Here, we analyzed for the first time the organic matrix of the aragonitic Sepia officinalis shell, with an emphasis on protein composition of two different structures: the dorsal shield and the chambered part. Our results highlight an organic matrix mainly composed of polysaccharide, glycoprotein and protein compounds as previously described in other mollusk shells, with quantitative and qualitative differences between the dorsal shield and the chamber part. Proteomic analysis resulted in identification of only a few protein compounds underlining the lack of reference databases for Sepiidae. However, most of them contain domains previously characterized in matrix proteins of aragonitic shell-builder mollusks, suggesting ancient and conserved mechanisms of the aragonite biomineralization processes within mollusks.

BIOLOGICAL SIGNIFICANCE: The cuttlefish{\textquoteright}s inner shell, better known under the name "cuttlebone", is a complex mineral structure unique in mollusks and involved in tissue support and buoyancy regulation. Although it combines useful properties as high compressive strength, high porosity and high permeability, knowledge about organic compounds involved in its building remains limited. Moreover, several cuttlebone organic matrix studies reported data very different from each other or from other mollusk shells. Thus, this study provides 1) an overview of the organization of the main mineral structures found in the S. officinalis shell, 2) a reliable baseline about its organic composition, and 3) a first descriptive proteomic approach of organic matrices found in the two main parts of this shell. These data will contribute to the general knowledge about mollusk biomineralization as well as in the identification of protein compounds involved in the Sepiidae shell calcification.

}, issn = {1876-7737}, doi = {10.1016/j.jprot.2016.08.015}, author = {Le Pabic, Charles and Marie, Arul and Marie, Benjamin and Percot, Aline and Laure Bonnaud-Ponticelli and Pascal Jean Lopez and Gilles Luquet} } @article {4377, title = {Characterisation of the mantle transcriptome and biomineralisation genes in the blunt-gaper clam, Mya truncata}, journal = {Marine Genomics}, volume = {27}, year = {2016}, pages = {47 - 55}, abstract = {

Abstract Members of the Myidae family are ecologically and economically important, but there is currently very little molecular data on these species. The present study sequenced and assembled the mantle transcriptome of Mya truncata from the North West coast of Scotland and identified candidate biomineralisation genes. RNA-Seq reads were assembled to create 20,106 contigs in a de novo transciptome, 18.81\% of which were assigned putative functions using \{BLAST\} sequence similarity searching (cuttoff E-value 1E {\quotesinglbase}{\`a}{\'\i} 10). The most highly expressed genes were compared to the Antarctic clam (Laternula elliptica) and showed that many of the dominant biological functions (muscle contraction, energy production, biomineralisation) in the mantle were conserved. There were however, differences in the constitutive expression of heat shock proteins, which were possibly due to the M. truncata sampling location being at a relatively low latitude, and hence relatively warm, in terms of the global distribution of the species. Phylogenetic analyses of the Tyrosinase proteins from M. truncata showed a gene expansion which was absent in L. elliptica. The tissue distribution expression patterns of putative biomineralisation genes were investigated using quantitative PCR, all genes showed a mantle specific expression pattern supporting their hypothesised role in shell secretion. The present study provides some preliminary insights into how clams from different environments {\quotesinglbase}{\"A}{\`\i} temperate versus polar {\quotesinglbase}{\"A}{\`\i} build their shells. In addition, the transcriptome data provides a valuable resource for future comparative studies investigating biomineralisation.

}, keywords = {shell}, issn = {1874-7787}, doi = {http://dx.doi.org/10.1016/j.margen.2016.01.003}, url = {http://www.sciencedirect.com/science/article/pii/S1874778716300034}, author = {Victoria A. Sleight and Michael A.S. Thorne and Lloyd S. Peck and Arivalagan, Jaison and Berland, Sophie and Marie, Arul and Melody S. Clark} } @article {4575, title = {Insights from the shell proteome: biomineralization to adaptation.}, journal = {Mol Biol Evol}, year = {2016}, month = {2016 Oct 15}, 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.

}, issn = {1537-1719}, doi = {10.1093/molbev/msw219}, author = {Arivalagan, Jaison and Yarra Teja and Marie, Benjamin and Sleight, Victoria A and Duvernois-Berthet, Evelyne and Clark, Melody S and Marie, Arul and Berland, Sophie} } @article {4270, title = {Shell matrix proteins of the clam, Mya truncata: Roles beyond shell formation through proteomic study}, journal = {Marine Genomics}, volume = {27}, year = {2016}, month = {06/2016}, pages = {69-74}, abstract = {

Abstract Mya truncata, a soft shell clam, is presented as a new model to study biomineralization through a proteomics approach. In this study, the shell and mantle tissue were analysed in order to retrieve knowledge about the secretion of shell matrix proteins (SMPs). Out of 67 and 127 shell and mantle proteins respectively, 16 were found in both shell and mantle. Bioinformatic analysis of \{SMP\} sequences for domain prediction revealed the presence of several new domains such as fucolectin tachylectin-4 pentraxin-1 (FTP), scavenger receptor, alpha-2-macroglobulin ({\OE}{\textpm}2 M), lipocalin and myosin tail along with previously reported \{SMP\} domains such as chitinase, carbonic anhydrase, tyrosinase, sushi, and chitin binding. Interestingly, these newly predicted domains are attributed with molecular functions other than biomineralization. These findings suggest that shells may not only act as protective armour from predatory action, but could also actively be related to other functions such as immunity. In this context, the roles of \{SMPs\} in biomineralization need to be looked in a new perspective.

}, keywords = {biomineralization}, issn = {1874-7787}, doi = {http://dx.doi.org/10.1016/j.margen.2016.03.005}, url = {http://www.sciencedirect.com/science/article/pii/S1874778716300186}, author = {Arivalagan, Jaison and Marie, Benjamin and Victoria A. Sleight and Melody S. Clark and Berland, Sophie and Marie, Arul} } @inbook {4068, title = {Unveiling the evolution of bivalve nacre proteins by shell proteomics of Unionoidae. }, booktitle = {Biomineralization: from fundamentals to biomaterials \& environmental issues}, volume = {672}, year = {2015}, pages = {pp.158-167}, edition = {Key Engineering Materials, 978-3-03835-591-5 Trans Tech Publications Ltd}, chapter = {2}, author = {Marie, Benjamin and Arivalagan, Jaison and Dubost, Lionel and Berland, Sophie and Marie, Arul and Marin, Fr{\'e}d{\'e}ric} }