scholarly journals Hydrophilic Shell Matrix Proteins of Nautilus pompilius and the Identification of a Core Set of Conchiferan Domains

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1925
Author(s):  
Davin H. E. Setiamarga ◽  
Kazuki Hirota ◽  
Masa-aki Yoshida ◽  
Yusuke Takeda ◽  
Keiji Kito ◽  
...  
Keyword(s):  
Matrix Protein ◽  
Phylogenetic Analyses ◽  
Protein Domains ◽  
Pearl Oyster ◽  
Matrix Proteins ◽  
Nautilus Pompilius ◽  
Shell Matrix ◽  
The Pacific ◽  
Major Shell ◽  
Shell Matrix Proteins

Despite being a member of the shelled mollusks (Conchiferans), most members of extant cephalopods have lost their external biomineralized shells, except for the basally diverging Nautilids. Here, we report the result of our study to identify major Shell Matrix Proteins and their domains in the Nautilid Nautilus pompilius, in order to gain a general insight into the evolution of Conchiferan Shell Matrix Proteins. In order to do so, we performed a multiomics study on the shell of N. pompilius, by conducting transcriptomics of its mantle tissue and proteomics of its shell matrix. Analyses of obtained data identified 61 distinct shell-specific sequences. Of the successfully annotated 27 sequences, protein domains were predicted in 19. Comparative analysis of Nautilus sequences with four Conchiferans for which Shell Matrix Protein data were available (the pacific oyster, the pearl oyster, the limpet and the Euhadra snail) revealed that three proteins and six protein domains were conserved in all Conchiferans. Interestingly, when the terrestrial Euhadra snail was excluded, another five proteins and six protein domains were found to be shared among the four marine Conchiferans. Phylogenetic analyses indicated that most of these proteins and domains were probably present in the ancestral Conchiferan, but employed in shell formation later and independently in most clades. Even though further studies utilizing deeper sequencing techniques to obtain genome and full-length sequences, and functional analyses, must be carried out in the future, our results here provide important pieces of information for the elucidation of the evolution of Conchiferan shells at the molecular level.

scholarly journals Hydrophilic Shell Matrix Proteins of Nautilus pompilius and The Identification of a Core Set of Conchiferan Domains

2020 ◽  
Author(s):  
Davin H. E. Setiamarga ◽  
Kazuki Hirota ◽  
Masa-aki Yoshida ◽  
Yusuke Takeda ◽  
Keiji Kito ◽  
...  
Keyword(s):  
Matrix Protein ◽  
Phylogenetic Analyses ◽  
Pearl Oyster ◽  
Matrix Proteins ◽  
Nautilus Pompilius ◽  
Shell Matrix ◽  
The Pacific ◽  
Major Shell ◽  
Shell Proteins ◽  
Shell Matrix Proteins

AbstractDespite being a member of the shelled mollusks (Conchiferans), most members of extant cephalopods have lost their external biomineralized shells, except for the Nautiloids. Here, we report the result of our study to identify major Shell Matrix Proteins and their domains in the Nautiloid Nautilus pompilius, in order to gain a general insight into the evolution of Conchiferan Shell Matrix Proteins. In order to do so, we conducted transcriptomics of the mantle, and proteomics of the shell of N. pompilius simultaneously. Analyses of obtained data identified 61 distinct shell-specific sequences. Of the successfully annotated 27 sequences, protein domains were predicted in 19. Comparative analysis of Nautilus sequences with four Conchiferans for which Shell Matrix Protein data were available (the pacific oyster, the pearl oyster, the limpet, and the Euhadra snail) revealed that three proteins and six domains of the shell proteins are conserved in all Conchiferans. Interestingly, when the terrestrial Euhadra snail was excluded, another five proteins and six domains were found to be shared among the four marine Conchiferans. Phylogenetic analyses indicated that most of these proteins and domains were present in the ancestral Conchiferan, but employed in shell formation later and independently in most clades. Although further studies utilizing deeper sequencing techniques to obtain genome and full-length sequences, and functional analyses, must be done in the future, our results here provide important pieces of information for the elucidation of the evolution of Conchiferan shells at the molecular level.

scholarly journals Shell matrix proteins - a potential tool for investigating the phylogenetic relationships of the Echinodermata

1992 ◽  
Vol 6 ◽  
pp. 236-236
Author(s):  
Emma S. Polson ◽  
J. Lawrence ◽  
L. L. Robbins
Keyword(s):  
Phylogenetic Relationships ◽  
Matrix Protein ◽  
Dna Analysis ◽  
Morphological Characters ◽  
Matrix Proteins ◽  
Molecular Weights ◽  
Shell Matrix ◽  
Shell Matrix Proteins ◽  
Luidia Clathrata ◽  
Mellita Tenuis

The phylogenetic relationships of the echinoderms remains controversial due to the traditional use of morphological characters which do not reflect convergent evolution. While biochemical techniques and DNA analysis may be used in addition to morphological characters for analysis of living echinoderms, these tools cannot be extended to fossils. Shell matrix proteins - of echinoderms may be trapped and preserved for millions of years in fossil genera.Analysis of shell matrix protein from Astropectin irregularis, Luidia clathrata and Mellita tenuis, reveal the presence of at least three major proteins of approximate molecular weights 230, 83 and 17 kDa common to all species. Astropectin irregularis showed four additional major bands of molecular weights 150, 90, 52 and 35 kDa along with at least 12 minor bands. Luidia clathrata showed five additional major bands of molecular weights 99, 60, 40, 24 and 21 kDa and at least 13 other minor bands. Mellita tenuis showed three additional bands of molecular weights 115, 96, and 24 kDa along with at least 4 minor bands.As the three common proteins have been found in both seastars (A. irregularis and L. clathrata) and echinoids (Mellita tenuis), further analysis of these shell matrix proteins may be used to elucidate phylogenetic relationships within the Echinodermata. In addition homoplasies may be identified and phylogenetically reassessed.

scholarly journals Temperature and Food Influence Shell Growth and Mantle Gene Expression of Shell Matrix Proteins in the Pearl Oyster Pinctada margaritifera

PLoS ONE ◽  
2014 ◽  
Vol 9 (8) ◽  
pp. e103944 ◽  
Author(s):  
Caroline Joubert ◽  
Clémentine Linard ◽  
Gilles Le Moullac ◽  
Claude Soyez ◽  
Denis Saulnier ◽  
...  
Keyword(s):  
Gene Expression ◽  
Shell Growth ◽  
Pearl Oyster ◽  
Matrix Proteins ◽  
Pinctada Margaritifera ◽  
Shell Matrix ◽  
Shell Matrix Proteins

scholarly journals Phylogenetic comparisons reveal mosaic histories of larval and adult shell matrix protein deployment in pteriomorph bivalves

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ran Zhao ◽  
Takeshi Takeuchi ◽  
Ryo Koyanagi ◽  
Alejandro Villar-Briones ◽  
Lixy Yamada ◽  
...  
Keyword(s):  
Matrix Protein ◽  
Phylogenetic Analyses ◽  
Organic Matrix ◽  
Pinctada Fucata ◽  
Chitin Binding Domain ◽  
Shell Matrix ◽  
Shell Matrix Protein ◽  
Shell Matrix Proteins ◽  
Factor Type ◽  
Von Willebrand

AbstractMolluscan shells are organo-mineral composites, in which the dominant calcium carbonate is intimately associated with an organic matrix comprised mainly of proteins and polysaccharides. However, whether the various shell matrix proteins (SMPs) date to the origin of hard skeletons in the Cambrian, or whether they represent later deployment through adaptive evolution, is still debated. In order to address this issue and to better understand the origins and evolution of biomineralization, phylogenetic analyses have been performed on the three SMP families, Von Willebrand factor type A (VWA) and chitin-binding domain-containing protein (VWA-CB dcp), chitobiase, and carbonic anhydrase (CA), which exist in both larval and adult shell proteomes in the bivalves, Crassostrea gigas and Pinctada fucata. In VWA-CB dcp and chitobiase, paralogs for larval and adult SMPs evolved before the divergence of these species. CA-SMPs have been taken as evidence for ancient origins of SMPs by their presumed indispensable function in biomineralization and ubiquitous distribution in molluscs. However, our results indicate gene duplications that gave rise to separate deployments as larval and adult CA-SMPs occurred independently in each lineage after their divergence, which is considerably more recent than hitherto assumed, supporting the “recent heritage and fast evolution” scenario for SMP evolution.

scholarly journals Independent adoptions of a set of proteins found in the matrix of the mineralized shell-like eggcase of Argonaut octopuses

2021 ◽  
Author(s):  
Davin H. E. Setiamarga ◽  
Kazuki Hirota ◽  
Risa Ikai ◽  
Seiji Imoto ◽  
Noriyoshi Sato ◽  
...  
Keyword(s):  
Draft Genome ◽  
Matrix Proteins ◽  
Mantle Tissue ◽  
Nautilus Pompilius ◽  
External Structure ◽  
Homologous Genes ◽  
Shell Matrix ◽  
The Matrix ◽  
Long Time ◽  
Shell Matrix Proteins

The Argonaut octopus, commonly called the paper nautilus, has a spiral-coiled shell-like eggcase. As the main characteristics, the eggcase has no internal septum, is composed entirely of calcite with chitosan being the main polycarbonate and is reportedly formed by organic materials secreted from the membranes of the arms. Meanwhile, the biomineralized external "true" shells of the Mollusks, which includes the Cephalopods, are secreted from the mantle tissue. Therefore, the histological origin of the two shells is completely different. The question of how the Argonauts, which phylogenetically diverged from the completely shell-less octopuses, could form a converging shell-like external structure has thus intrigued biologists for a long time. To answer this question, we performed a multi-omics analysis of the transcriptome and proteome of the two congeneric Argonaut species, Argonauta argo and A. hians. Our result indicates that the shell-like eggcase is not a homolog of the shell, even at the protein level, because the Argonauts apparently recruited a different set of protein repertoires to as eggcase matrix proteins (EcMPs). However, we also found the homologs of three shell matrix proteins (SMPs) of the Conchiferan Mollusks, Pif-like, SOD, and TRX, in the eggcase matrix. The proteins were also found in the only surviving shelled Cephalopods, the nautiloid Nautilus pompilius. Phylogenetic analysis revealed that homologous genes of the Conchiferan SMPs and EcMPs were found in the draft genome of shell-less octopuses. Our result reported here thus suggests that the SMP-coding genes are conserved in both shelled and shell-less Cephalopods. Meanwhile, the Argonauts adopted some of the SMP-coding genes and other non-SMP-coding genes, to form a convergent, non-homologous biomineralized external structure, the eggcase, which is autapomorphic to the group.

The Diversity of Shell Matrix Proteins: Genome-Wide Investigation of the Pearl Oyster, Pinctada fucata

2013 ◽  
Vol 30 (10) ◽  
pp. 801 ◽  
Author(s):  
Hiroshi Miyamoto ◽  
Hirotoshi Endo ◽  
Naoki Hashimoto ◽  
Kurin limura ◽  
Yukinobu Isowa ◽  
...  
Keyword(s):  
Pearl Oyster ◽  
Pinctada Fucata ◽  
Matrix Proteins ◽  
Shell Matrix ◽  
Genome Wide ◽  
Shell Matrix Proteins

scholarly journals PU14, a Novel Matrix Protein, Participates in Pearl Oyster, Pinctada Fucata, Shell Formation

2021 ◽  
Author(s):  
Yinghui Ji ◽  
Xue Yang ◽  
Dong Yang ◽  
Rongqing Zhang
Keyword(s):  
Matrix Protein ◽  
Pinctada Fucata ◽  
Matrix Proteins ◽  
In Vitro Experiments ◽  
Shell Formation ◽  
Prismatic Layer ◽  
Shell Matrix ◽  
Shell Matrix Proteins ◽  
Functional Analyses

AbstractBiomineralization is a widespread biological process, involved in the formation of shells, teeth, and bones. Shell matrix proteins have been widely studied for their importance during shell formation. In 2015, our group identified 72 unique shell matrix proteins in Pinctada fucata, among which PU14 is a matrix protein detected in the soluble fraction that solely exists in the prismatic layer. However, the function of PU14 is still unclear. In this study, the full-length cDNA sequence of PU14 was obtained and functional analyses of PU14 protein during shell formation were performed. The deduced protein has a molecular mass of 77.8 kDa and an isoelectric point of 11.34. The primary protein structure contains Gln-rich and random repeat units, which are typical characteristics of matrix protein and indicate its potential function during shell formation. In vivo and in vitro experiments indicated PU14 has prismatic layer functions during shell formation. The tissue expression patterns showed that PU14 was mainly expressed in the mantle tissue, which is consistent with prismatic layer formation. Notching experiments suggested that PU14 responded to repair and regenerate the injured shell. After inhibiting gene expression by injecting PU14-specific double-stranded RNA, the inner surface of the prismatic layer changed significantly and became rougher. Further, in vitro experiments showed that recombinant protein rPU14 impacted calcite crystal morphology. Taken together, characterization and functional analyses of a novel matrix protein, PU14, provide new insights about basic matrix proteins and their functions during shell formation.

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