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Liao Z, Liu F, Wang Y, Fan X, Li Y, He J, Buttino I, Yan X, Zhang X, Shi G. Transcriptomic response of Mytilus coruscus mantle to acute sea water acidification and shell damage. Front Physiol 2023; 14:1289655. [PMID: 37954445 PMCID: PMC10639161 DOI: 10.3389/fphys.2023.1289655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/16/2023] [Indexed: 11/14/2023] Open
Abstract
Mytilus coruscus is an economically important marine calcifier living in the Yangtze River estuary sea area, where seasonal fluctuations in natural pH occur owing to freshwater input, resulting in a rapid reduction in seawater pH. In addition, Mytilus constantly suffers from shell fracture or injury in the natural environment, and the shell repair mechanisms in mussels have evolved to counteract shell injury. Therefore, we utilized shell-complete and shell-damaged Mytilus coruscus in this study and performed transcriptomic analysis of the mantle to investigate whether the expression of mantle-specific genes can be induced by acute seawater acidification and how the mantle responds to acute acidification during the shell repair process. We found that acute acidification induced more differentially expressed genes than shell damage in the mantle, and the biomineralization-related Gene Ontology terms and KEGG pathways were significantly enriched by these DEGs. Most DEGs were upregulated in enriched pathways, indicating the activation of biomineralization-related processes in the mussel mantle under acute acidification. The expression levels of some shell matrix proteins and antimicrobial peptides increased under acute acidification and/or shell damage, suggesting the molecular modulation of the mantle for the preparation and activation of the shell repairing and anti-infection under adverse environmental conditions. In addition, morphological and microstructural analyses were performed for the mantle edge and shell cross-section, and changes in the mantle secretory capacity and shell inner film system induced by the two stressors were observed. Our findings highlight the adaptation of M. coruscus in estuarine areas with dramatic fluctuations in pH and may prove instrumental in its ability to survive ocean acidification.
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Affiliation(s)
- Zhi Liao
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Fei Liu
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Ying Wang
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Xiaojun Fan
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Yingao Li
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Jianyu He
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Isabella Buttino
- Italian Institute for Environmental Protection and Research (ISPRA), Livorno, Italy
| | - Xiaojun Yan
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Xiaolin Zhang
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Ge Shi
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
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Shimizu K, Negishi L, Ito T, Touma S, Matsumoto T, Awaji M, Kurumizaka H, Yoshitake K, Kinoshita S, Asakawa S, Suzuki M. Evolution of nacre- and prisms-related shell matrix proteins in the pen shell, Atrina pectinata. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 44:101025. [PMID: 36075178 DOI: 10.1016/j.cbd.2022.101025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 01/27/2023]
Abstract
The molluscan shell is a good model for understanding the mechanisms underlying biomineralization. It is composed of calcium carbonate crystals and many types of organic molecules, such as the matrix proteins, polysaccharides, and lipids. The pen shell Atrina pectinata (Pterioida, Pinnidae) has two shell microstructures: an outer prismatic layer and an inner nacreous layer. Similar microstructures are well known in pearl oysters (Pteriidae), such as Pinctada fucata, and many kinds of shell matrix proteins (SMPs) have been identified from their shells. However, the members of SMPs that consist of the nacreous and prismatic layers of Pinnidae bivalves remain unclear. In this study, we identified 114 SMPs in the nacreous and prismatic layers of A. pectinata, of which only seven were found in both microstructures. 54 of them were found to bind calcium carbonate. Comparative analysis of nine molluscan shell proteomes showed that 69 of 114 SMPs of A. pectinata were found to have sequential similarity with at least one or more SMPs of other molluscan species. For instance, nacrein, tyrosinase, Pif/BMSP-like, chitinase (CN), chitin-binding proteins, CD109, and Kunitz-type serine proteinase inhibitors are widely shared among bivalves and gastropods. Our results provide new insights for understanding the complex evolution of SMPs related to nacreous and prismatic layer formation in the pteriomorph 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
| | - Lumi Negishi
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Takumi Ito
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Shogo Touma
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Toshie Matsumoto
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, 422-1 Nakatsuhama, Minami-Ise, Watarai, Mie 516-0193, Japan
| | - Masahiko Awaji
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, 422-1 Nakatsuhama, Minami-Ise, Watarai, Mie 516-0193, Japan
| | - Hitoshi Kurumizaka
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Kazutoshi Yoshitake
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Shigeharu Kinoshita
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, 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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McElroy KE, Bankers L, Soper D, Hehman G, Boore JL, Logsdon JM, Neiman M. Patterns of gene expression in ovaries of sexual vs. asexual lineages of a freshwater snail. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.845640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Why sexual reproduction is so common when asexual reproduction should be much more efficient and less costly remains an open question in evolutionary biology. Comparisons between otherwise similar sexual and asexual taxa allow us to characterize the genetic architecture underlying asexuality, which can, in turn, illuminate how this reproductive mode transition occurred and the mechanisms by which it is maintained or disrupted. Here, we used transcriptome sequencing to compare patterns of ovarian gene expression between actively reproducing obligately sexual and obligately asexual females from multiple lineages of Potamopyrgus antipodarum, a freshwater New Zealand snail characterized by frequent separate transitions to asexuality and coexistence of otherwise similar sexual and asexual lineages. We also used these sequence data to evaluate whether population history accounts for variation in patterns of gene expression. We found that source population was a major source of gene expression variation, and likely more influential than reproductive mode. This outcome for these common garden-raised snails is strikingly similar to earlier results from field-collected snails. While we did not identify a likely set of candidate genes from expression profiles that could plausibly explain how transitions to asexuality occurred, we identified around 1,000 genes with evidence of differential expression between sexual and asexual reproductive modes, and 21 genes that appear to exhibit consistent expression differences between sexuals and asexuals across genetic backgrounds. This second smaller set of genes provides a good starting point for further exploration regarding a potential role in the transition to asexual reproduction. These results mark the first effort to characterize the causes of asexuality in P. antipodarum, demonstrate the apparently high heritability of gene expression patterns in this species, and hint that for P. antipodarum, transitions to asexuality might not necessarily be strongly associated with broad changes in gene expression.
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Yarra T, Ramesh K, Blaxter M, Hüning A, Melzner F, Clark MS. Transcriptomic analysis of shell repair and biomineralization in the blue mussel, Mytilus edulis. BMC Genomics 2021; 22:437. [PMID: 34112105 PMCID: PMC8194122 DOI: 10.1186/s12864-021-07751-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 05/27/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Biomineralization by molluscs involves regulated deposition of calcium carbonate crystals within a protein framework to produce complex biocomposite structures. Effective biomineralization is a key trait for aquaculture, and animal resilience under future climate change. While many enzymes and structural proteins have been identified from the shell and in mantle tissue, understanding biomieralization is impeded by a lack of fundamental knowledge of the genes and pathways involved. In adult bivalves, shells are secreted by the mantle tissue during growth, maintenance and repair, with the repair process, in particular, amenable to experimental dissection at the transcriptomic level in individual animals. RESULTS Gene expression dynamics were explored in the adult blue mussel, Mytilus edulis, during experimentally induced shell repair, using the two valves of each animal as a matched treatment-control pair. Gene expression was assessed using high-resolution RNA-Seq against a de novo assembled database of functionally annotated transcripts. A large number of differentially expressed transcripts were identified in the repair process. Analysis focused on genes encoding proteins and domains identified in shell biology, using a new database of proteins and domains previously implicated in biomineralization in mussels and other molluscs. The genes implicated in repair included many otherwise novel transcripts that encoded proteins with domains found in other shell matrix proteins, as well as genes previously associated with primary shell formation in larvae. Genes with roles in intracellular signalling and maintenance of membrane resting potential were among the loci implicated in the repair process. While haemocytes have been proposed to be actively involved in repair, no evidence was found for this in the M. edulis data. CONCLUSIONS The shell repair experimental model and a newly developed shell protein domain database efficiently identified transcripts involved in M. edulis shell production. In particular, the matched pair analysis allowed factoring out of much of the inherent high level of variability between individual mussels. This snapshot of the damage repair process identified a large number of genes putatively involved in biomineralization from initial signalling, through calcium mobilization to shell construction, providing many novel transcripts for future in-depth functional analyses.
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Affiliation(s)
- Tejaswi Yarra
- Ashworth Laboratories, University of Edinburgh, Institute of Evolutionary Biology, Charlotte Auerbach Road, EH9 3FL, Edinburgh, UK
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, CB3 0ET, Cambridge, UK
| | - Kirti Ramesh
- GEOMAR Helmholtz Centre for Ocean Research, 24105, Kiel, Germany
| | - Mark Blaxter
- Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, Saffron Walden, UK
| | - Anne Hüning
- GEOMAR Helmholtz Centre for Ocean Research, 24105, Kiel, Germany
| | - Frank Melzner
- GEOMAR Helmholtz Centre for Ocean Research, 24105, Kiel, Germany
| | - Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, CB3 0ET, Cambridge, UK.
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The mantle exosome proteins of Hyriopsis cumingii participate in shell and nacre color formation. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 39:100844. [PMID: 33971400 DOI: 10.1016/j.cbd.2021.100844] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/30/2021] [Accepted: 04/23/2021] [Indexed: 12/13/2022]
Abstract
Pearl color is closely related to the nacre color of shell in Hyriopsis cumingii, and pearl color has a huge impact on its price. The nacre is an important part of the shell, and studies have suggested that mantle exosomes participated in shell formation. Exosomes contain many different proteins that are involved in different biological processes. In this study, exosomes were extracted from mantles of mussels with different nacre color. TMT quantitative proteome sequencing analysis was performed on purple and white mussel mantle exosomes, and 4861 proteins were obtained. Based on the standard of (|log2 (Fold change)| ≥ 1.2 or ≤ 0.83 and p-value ≤ 0.05), a total of 758 differentially expressed proteins were found. Some proteins involved in shell and nacre color formation were predicted with the proteins annotate, GO classification system. Moreover, 14 differentially expressed proteins (including eight up-regulated proteins and six down-regulated proteins) were validated using parallel reaction monitoring (PRM) assays. Overall, this information will be useful to improve our understanding of the molecular mechanisms of shell and nacre color formation in H. cumingii.
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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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Arivalagan J, Marie B, Chiappetta G, Vinh J, Gallet X, Lebon M, M'Zoudi S, Dubois P, Berland S, Marie A. Deciphering shell proteome within different Baltic populations of mytilid mussels illustrates important local variability and potential consequences in the context of changing marine conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 745:140878. [PMID: 32721612 DOI: 10.1016/j.scitotenv.2020.140878] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/06/2020] [Accepted: 07/08/2020] [Indexed: 06/11/2023]
Abstract
Molluscs defend themselves against predation and environmental stressors through the possession of mineralized shells. Mussels are widely used to predict the effects of abiotic factors such as salinity and pH on marine calcifiers in the context of changing ocean conditions. Shell matrix proteins are part of the molecular control regulating the biomineralization processes underpinning shell production. Under changing environmental conditions, differential expression of these proteins leads to the phenotypic plasticity of shells seen in many mollusc species. Low salinity decreases the availability of calcium and inorganic carbon in seawater and consequently energetic constraints often lead to thin, small and fragile shells in Mytilid mussels inhabiting Baltic Sea. To understand how the modulation of shell matrix proteins alters biomineralization, we compared the shell proteomes of mussels living under full marine conditions in the North Sea to those living in the low saline Baltic Sea. Modulation of proteins comprising the Mytilus biomineralization tool kit is observed. These data showed a relative increase in chitin related proteins, decrease in SD-rich, GA-rich shell matrix proteins indicating that altered protein scaffolding and mineral nucleation lead to impaired shell microstructures influencing shell resistance in Baltic Mytilid mussels. Interestingly, proteins with immunity domains in the shell matrix are also found to be modulated. Shell traits such as periostracum thickness, organic content and fracture resistance qualitatively correlates with the modulation of SMPs in Mytilid mussels providing key insights into control of biomineralization at molecular level in the context of changing marine conditions.
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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, 75005 Paris, France; UMR 7208 CNRS/MNHN/UPMC/IRD Biologie des Organismes Aquatiques et Ecosystèmes, Sorbonne Universités, Muséum national d'Histoire naturelle, 75005 Paris, France
| | - Benjamin Marie
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Sorbonne Universités, Muséum national d'Histoire naturelle, 75005 Paris, France
| | | | - Joëlle Vinh
- USR3149, ESPCI ParisTech, 75005 Paris, France
| | - Xavier Gallet
- UMR 7194, Département de préhistoire, Musée de l'Homme, 75116 Paris, France
| | - Matthieu Lebon
- UMR 7194, Département de préhistoire, Musée de l'Homme, 75116 Paris, France
| | - Saloua M'Zoudi
- Laboratoire de Biologie marine CP160/15, Université Libre de Bruxelles, B-1050 Bruxelles, Belgium
| | - Philippe Dubois
- Laboratoire de Biologie marine CP160/15, Université Libre de Bruxelles, B-1050 Bruxelles, Belgium
| | - Sophie Berland
- UMR 7208 CNRS/MNHN/UPMC/IRD Biologie des Organismes Aquatiques et Ecosystèmes, Sorbonne Universités, Muséum national d'Histoire naturelle, 75005 Paris, France
| | - Arul Marie
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Sorbonne Universités, Muséum national d'Histoire naturelle, 75005 Paris, France.
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Kintsu H, Nishimura R, Negishi L, Kuriyama I, Tsuchihashi Y, Zhu L, Nagata K, Suzuki M. Identification of methionine -rich insoluble proteins in the shell of the pearl oyster, Pinctada fucata. Sci Rep 2020; 10:18335. [PMID: 33110152 PMCID: PMC7591529 DOI: 10.1038/s41598-020-75444-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/12/2020] [Indexed: 11/30/2022] Open
Abstract
The molluscan shell is a biomineral that comprises calcium carbonate and organic matrices controlling the crystal growth of calcium carbonate. The main components of organic matrices are insoluble chitin and proteins. Various kinds of proteins have been identified by solubilizing them with reagents, such as acid or detergent. However, insoluble proteins remained due to the formation of a solid complex with chitin. Herein, we identified these proteins from the nacreous layer, prismatic layer, and hinge ligament of Pinctada fucata using mercaptoethanol and trypsin. Most identified proteins contained a methionine-rich region in common. We focused on one of these proteins, NU-5, to examine the function in shell formation. Gene expression analysis of NU-5 showed that NU-5 was highly expressed in the mantle, and a knockdown of NU-5 prevented the formation of aragonite tablets in the nacre, which suggested that NU-5 was required for nacre formation. Dynamic light scattering and circular dichroism revealed that recombinant NU-5 had aggregation activity and changed its secondary structure in the presence of calcium ions. These findings suggest that insoluble proteins containing methionine-rich regions may be important for scaffold formation, which is an initial stage of biomineral formation.
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Affiliation(s)
- Hiroyuki Kintsu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Center for Health and Environmental Risk Research, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba-city, Ibaraki, 305-8506, Japan
| | - Ryo Nishimura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Lumi Negishi
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Isao Kuriyama
- Mie Prefecture Fisheries Research Institute, 3564-3 Hamajima, Hamajima-cho, Shima-city, Mie, 517-0404, Japan
| | - Yasushi Tsuchihashi
- Mie Prefecture Fisheries Research Institute, 3564-3 Hamajima, Hamajima-cho, Shima-city, Mie, 517-0404, Japan
| | - Lingxiao Zhu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Koji Nagata
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Michio Suzuki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
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9
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Clark MS, Peck LS, Arivalagan J, Backeljau T, Berland S, Cardoso JCR, Caurcel C, Chapelle G, De Noia M, Dupont S, Gharbi K, Hoffman JI, Last KS, Marie A, Melzner F, Michalek K, Morris J, Power DM, Ramesh K, Sanders T, Sillanpää K, Sleight VA, Stewart-Sinclair PJ, Sundell K, Telesca L, Vendrami DLJ, Ventura A, Wilding TA, Yarra T, Harper EM. Deciphering mollusc shell production: the roles of genetic mechanisms through to ecology, aquaculture and biomimetics. Biol Rev Camb Philos Soc 2020; 95:1812-1837. [PMID: 32737956 DOI: 10.1111/brv.12640] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/17/2020] [Accepted: 07/17/2020] [Indexed: 12/20/2022]
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 CaCO3 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 CaCO3 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.
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Affiliation(s)
- Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, U.K
| | - Lloyd S Peck
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, U.K
| | - Jaison Arivalagan
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France.,Proteomics Center of Excellence, Northwestern University, 710 N Fairbanks Ct, Chicago, IL, U.S.A
| | - Thierry Backeljau
- Royal Belgian Institute of Natural Sciences, Rue Vautier 29, Brussels, B-1000, Belgium.,Evolutionary Ecology Group, University of Antwerp, Universiteitsplein 1, Antwerp, B-2610, Belgium
| | - Sophie Berland
- UMR 7208 CNRS/MNHN/UPMC/IRD Biologie des Organismes Aquatiques et Ecosystèmes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Joao C R Cardoso
- Centro de Ciencias do Mar, Universidade do Algarve, Campus de Gambelas, Faro, 8005-139, Portugal
| | - Carlos Caurcel
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, U.K
| | - Gauthier Chapelle
- Royal Belgian Institute of Natural Sciences, Rue Vautier 29, Brussels, B-1000, Belgium
| | - Michele De Noia
- Department of Animal Behavior, University of Bielefeld, Postfach 100131, Bielefeld, 33615, Germany.,Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, U.K
| | - Sam Dupont
- Department of Biological and Environmental Sciences, University of Göteburg, Box 463, Göteburg, SE405 30, Sweden
| | - Karim Gharbi
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, U.K
| | - Joseph I Hoffman
- Department of Animal Behavior, University of Bielefeld, Postfach 100131, Bielefeld, 33615, Germany
| | - Kim S Last
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, Argyll, PA37 1QA, U.K
| | - Arul Marie
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Frank Melzner
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, 24105, Germany
| | - Kati Michalek
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, Argyll, PA37 1QA, U.K
| | - James Morris
- Royal Belgian Institute of Natural Sciences, Rue Vautier 29, Brussels, B-1000, Belgium
| | - Deborah M Power
- Centro de Ciencias do Mar, Universidade do Algarve, Campus de Gambelas, Faro, 8005-139, Portugal
| | - Kirti Ramesh
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, 24105, Germany
| | - Trystan Sanders
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, 24105, Germany
| | - Kirsikka Sillanpää
- Swemarc, Department of Biological and Environmental Science, University of Gothenburg, Box 463, Gothenburg, SE405 30, Sweden
| | - Victoria A Sleight
- School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, U.K
| | | | - Kristina Sundell
- Swemarc, Department of Biological and Environmental Science, University of Gothenburg, Box 463, Gothenburg, SE405 30, Sweden
| | - Luca Telesca
- Department of Earth Sciences, University of Cambridge, Cambridge, CB2 3EQ, U.K
| | - David L J Vendrami
- Department of Animal Behavior, University of Bielefeld, Postfach 100131, Bielefeld, 33615, Germany
| | - Alexander Ventura
- Department of Biological and Environmental Sciences, University of Göteburg, Box 463, Göteburg, SE405 30, Sweden
| | - Thomas A Wilding
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, Argyll, PA37 1QA, U.K
| | - Tejaswi Yarra
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, U.K.,Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, U.K
| | - Elizabeth M Harper
- Department of Earth Sciences, University of Cambridge, Cambridge, CB2 3EQ, U.K
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10
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Oudot M, Neige P, Shir IB, Schmidt A, Strugnell JM, Plasseraud L, Broussard C, Hoffmann R, Lukeneder A, Marin F. The shell matrix and microstructure of the Ram’s Horn squid: Molecular and structural characterization. J Struct Biol 2020; 211:107507. [DOI: 10.1016/j.jsb.2020.107507] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 12/11/2022]
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11
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Sakalauskaite J, Plasseraud L, Thomas J, Albéric M, Thoury M, Perrin J, Jamme F, Broussard C, Demarchi B, Marin F. The shell matrix of the european thorny oyster, Spondylus gaederopus: microstructural and molecular characterization. J Struct Biol 2020; 211:107497. [PMID: 32220629 DOI: 10.1016/j.jsb.2020.107497] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/20/2020] [Accepted: 03/22/2020] [Indexed: 11/18/2022]
Abstract
Molluscs, the largest marine phylum, display extraordinary shell diversity and sophisticated biomineral architectures. However, mineral-associated biomolecules involved in biomineralization are still poorly characterised. We report the first comprehensive structural and biomolecular study of Spondylus gaederopus, a pectinoid bivalve with a peculiar shell texture. Used since prehistoric times, this is the best-known shell of Europe's cultural heritage. We find that Spondylus microstructure is very poor in mineral-bound organics, which are mostly intercrystalline and concentrated at the interface between structural layers. Using high-resolution liquid chromatography tandem mass spectrometry (LC-MS/MS) we characterized several shell protein fractions, isolated following different bleaching treatments. Several peptides were identified as well as six shell proteins, which display features and domains typically found in biomineralized tissues, including the prevalence of intrinsically disordered regions. It is very likely that these sequences only partially represent the full proteome of Spondylus, considering the lack of genomics data for this genus and the fact that most of the reconstructed peptides do not match with any known shell proteins, representing consequently lineage-specific sequences. This work sheds light onto the shell matrix involved in the biomineralization in spondylids. Our proteomics data suggest that Spondylus has evolved a shell-forming toolkit, distinct from that of other better studied pectinoids - fine-tuned to produce shell structures with high mechanical properties, while limited in organic content. This study therefore represents an important milestone for future studies on biomineralized skeletons and provides the first reference dataset for forthcoming molecular studies of Spondylus archaeological artifacts.
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Affiliation(s)
- Jorune Sakalauskaite
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Turin, Italy; Biogeosciences, UMR CNRS 6282, University of Burgundy-Franche-Comté (UBFC), 6 Boulevard Gabriel, 21000 Dijon, France.
| | - Laurent Plasseraud
- Institute of Molecular Chemistry, ICMUB UMR CNRS 6302, University of Burgundy-Franche-Comté (UBFC), 9 Avenue Alain Savary, 21000 Dijon, France
| | - Jérôme Thomas
- Biogeosciences, UMR CNRS 6282, University of Burgundy-Franche-Comté (UBFC), 6 Boulevard Gabriel, 21000 Dijon, France
| | - Marie Albéric
- Laboratoire Chimie de la Matière Condensée de Paris, UMR, CNRS 7574, Sorbonne Université, Place Jussieu 4, 75252 Paris, France
| | - Mathieu Thoury
- IPANEMA, CNRS, ministère de la Culture, UVSQ, USR3461, Université Paris-Saclay, F-91192 Gif-sur-Yvette, France
| | - Jonathan Perrin
- Synchrotron SOLEIL, L'Orme des Merisiers, 91192 Gif sur Yvette Cedex, France
| | - Frédéric Jamme
- Synchrotron SOLEIL, L'Orme des Merisiers, 91192 Gif sur Yvette Cedex, France
| | - Cédric Broussard
- 3P5 Proteomic Platform, University of Paris, Cochin Institute, INSERM, U1016, CNRS, UMR8104, F-75014 Paris, France
| | - Beatrice Demarchi
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Turin, Italy
| | - Frédéric Marin
- Biogeosciences, UMR CNRS 6282, University of Burgundy-Franche-Comté (UBFC), 6 Boulevard Gabriel, 21000 Dijon, France.
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12
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13
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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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