Evolution of nacre- and prisms-related shell matrix proteins in the pen shell, Atrina pectinata

Shimizu, Keisuke; Negishi, Lumi; Ito, Tetsuo; Touma, Shogo; Matsumoto, Takanori; Awaji, Masahiko; Kurumizaka, Hitoshi; Yoshitake, Kazutoshi; Kinoshita, Shigeharu; Asakawa, Shuichi; Suzuki, Michio

doi:10.1016/j.cbd.2022.101025

Cited by 7 publications

(4 citation statements)

References 76 publications

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“…2 d). These domains were chitin-binding (CB) and von Willebrand factor type A (VWA), which were also classified as the members of molluscan biomineralization toolkit in previous studies [ 10 , 15 , 30 , 49 , 56 , 61 ]. Based on these two domains, various SMPs were clustered into an orthogroup (OG0000000) which was shared by the shell proteomes of seven molluscs (Additional file 1 : Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Major proteins and the best matches of minor proteins were identified as SMPs of C. nippona in this study. Furthermore, SMPs of the other six molluscs including C. gigas [ 30 ], Atrina pectinata [ 15 ], Tridacna crocea [ 121 ], P. fucata [ 30 ], Lottia gigantea [ 122 ], and N. pompilius [ 49 ] were download and used for comparative analysis of shell proteomes. Functional domain annotations of SMPs were performed by searching against various databases, including SMART, CDD, Pfam, PROSITE patterns, PROSITE profiles, and SUPERFAMILY, using InterProScan (v 5.52–86.0) [ 101 ].…”

Section: Methodsmentioning

confidence: 99%

“…Despite the conservation of shell morphology within many taxa, ultrastructural and molecular analyses have revealed that shell microstructures have evolved independently multiple times across various molluscan lineages [ 2 , 13 ]. At the proteomic level, a distinct partitioning of SMPs has been observed among different shell microstructures [ 6 , 14 , 15 ]. Interestingly, similar shell microstructures in different molluscs are comprised of markedly distinct proteins [ 16 , 17 ].…”

Section: Introductionmentioning

confidence: 99%

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Multi-omic insights into the formation and evolution of a novel shell microstructure in oysters

Bai,

Liu,

et al. 2023

BMC Biol

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Background Molluscan shell, composed of a diverse range of architectures and microstructures, is a classic model system to study the relationships between molecular evolution and biomineralized structure formation. The shells of oysters differ from those of other molluscs by possessing a novel microstructure, chalky calcite, which facilitates adaptation to the sessile lifestyle. However, the genetic basis and evolutionary origin of this adaptive innovation remain largely unexplored. Results We report the first whole-genome assembly and shell proteomes of the Iwagaki oyster Crassostrea nippona. Multi-omic integrative analyses revealed that independently expanded and co-opted tyrosinase, peroxidase, TIMP genes may contribute to the chalky layer formation in oysters. Comparisons with other molluscan shell proteomes imply that von Willebrand factor type A and chitin-binding domains are basic members of molluscan biomineralization toolkit. Genome-wide identification and analyses of these two domains in 19 metazoans enabled us to propose that the well-known Pif may share a common origin in the last common ancestor of Bilateria. Furthermore, Pif and LamG3 genes acquire new genetic function for shell mineralization in bivalves and the chalky calcite formation in oysters likely through a combination of gene duplication and domain reorganization. Conclusions The spatial expression of SMP genes in the mantle and molecular evolution of Pif are potentially involved in regulation of the chalky calcite deposition, thereby shaping the high plasticity of the oyster shell to adapt to a sessile lifestyle. This study further highlights neo-functionalization as a crucial mechanism for the diversification of shell mineralization and microstructures in molluscs, which may be applied more widely for studies on the evolution of metazoan biomineralization.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Multi-omic insights into the formation and evolution of a novel shell microstructure in oysters

Bai,

Liu,

et al. 2023

BMC Biol

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“…Indeed, recent high-throughput screening, combining transcriptomics on mollusc mantle and proteomics on shell extracts, has shown that the shell matrix is composed of tens-not to say hundreds-of proteins that can be classified in several families [9][10][11]. While many proteins, in particular those with low-complexity domains (LCDs) are orphans of functions, others exhibit amino acid sequences that bring them close to bioactive factors of interest, such as bactericides, signalling molecules or protease inhibitors [12,13]. Today, shell proteins, and more generally shell macromolecules, are considered as a potential reservoir of useful substances, not only in biomaterials domain, but also in health research, aquaculture, and zootechnics [9,14].…”

Section: Introductionmentioning

confidence: 99%

Diverting the Use of Hand-Operated Tablet Press Machines to Bioassays: A Novel Protocol to Test ‘Waste’ Insoluble Shell Matrices

Lutet-Toti,

Da Silva Feliciano,

Debrosse

et al. 2024

MPs

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To mineralize their shells, molluscs secrete a complex cocktail of proteins—collectively defined as the calcifying shell matrix—that remains occluded in the exoskeleton. Nowadays, protein extracts from shells are recognized as a potential source of bioactive substances, among which signalling molecules, bactericides or protease inhibitors offer the most tangible perspectives in applied sciences, health, and aquaculture. However, one technical obstacle in testing the activity of shell extracts lies in their high insolubility. In this paper, we present a protocol that circumvents this impediment. After an adapted shell protein extraction and the production of two organic fractions—one soluble, one insoluble—we employ a hand-operated tablet press machine to generate well-calibrated tablets composed of 100% insoluble shell matrix. FT-IR monitoring of the quality of the tablets shows that the pressure used in the press machine does not impair the molecular properties of the insoluble extracts. The produced tablets can be directly tested in different biological assays, such as the bactericidal inhibition zone assay in Petri dish, as illustrated here. Diverting the use of the hand-operated tablet press opens new perspectives in the analysis of insoluble shell matrices, for discovering novel bioactive components.

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Comparative proteomics of the shell matrix proteins of Nautilus pompilius and the conchiferans provide insights into mollusk shell evolution at the molecular level

Hirota,

Tochino,

Seto

et al. 2023

Mar Biol

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Evolution of nacre- and prisms-related shell matrix proteins in the pen shell, Atrina pectinata

Cited by 7 publications

References 76 publications

Multi-omic insights into the formation and evolution of a novel shell microstructure in oysters

Multi-omic insights into the formation and evolution of a novel shell microstructure in oysters

Diverting the Use of Hand-Operated Tablet Press Machines to Bioassays: A Novel Protocol to Test ‘Waste’ Insoluble Shell Matrices

Comparative proteomics of the shell matrix proteins of Nautilus pompilius and the conchiferans provide insights into mollusk shell evolution at the molecular level

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