scholarly journals Biochemical and molecular characterization of N66 from the shell ofPinctada mazatlanica

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7212
Author(s):  
Crisalejandra Rivera-Perez ◽  
Catalina Magallanes-Dominguez ◽  
Rosa Virginia Dominguez-Beltran ◽  
Josafat Jehu Ojeda-Ramirez de Areyano ◽  
Norma Y. Hernandez-Saavedra
Keyword(s):  
Posttranslational Modifications ◽  
Protein A ◽  
Pearl Oyster ◽  
Peptide Sequence ◽  
Calcium Carbonate Precipitation ◽  
Base Pairs ◽  
Shell Matrix ◽  
Glycosylation Sites ◽  
Shell Matrix Proteins

Mollusk shell mineralization is a tightly controlled process made by shell matrix proteins (SMPs). However, the study of SMPs has been limited to a few model species. In this study, the N66 mRNA of the pearl oysterPinctada mazatlanicawas cloned and functionally characterized. The full sequence of the N66 mRNA comprises 1,766 base pairs, and encodes one N66 protein. A sequence analysis revealed that N66 contained two carbonic anhydrase (CA) domains, a NG domain and several glycosylation sites. The sequence showed similarity to the CA VII but also with its homolog protein nacrein. The native N66 protein was isolated from the shell and identified by mass spectrometry, the peptide sequence matched to the nucleotide sequence obtained. Native N66 is a glycoprotein with a molecular mass of 60–66 kDa which displays CA activity and calcium carbonate precipitation ability in presence of different salts. Also, a recombinant form of N66 was produced inEscherichia coli, and functionally characterized. The recombinant N66 displayed higher CA activity and crystallization capability than the native N66, suggesting that the lack of posttranslational modifications in the recombinant N66 might modulate its activity.

scholarly journals In Silico Proteome Cleavage Reveals Iterative Digestion Strategy for High Sequence Coverage

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Jesse G. Meyer
Keyword(s):  
Posttranslational Modifications ◽  
Rna Splicing ◽  
Shotgun Proteomics ◽  
Peptide Sequence ◽  
Sequence Coverage ◽  
Proteome Coverage ◽  
Protein Inference ◽  
Peptide Length ◽  
Splicing Variants

In the postgenome era, biologists have sought to measure the complete complement of proteins, termed proteomics. Currently, the most effective method to measure the proteome is with shotgun, or bottom-up, proteomics, in which the proteome is digested into peptides that are identified followed by protein inference. Despite continuous improvements to all steps of the shotgun proteomics workflow, observed proteome coverage is often low; some proteins are identified by a single peptide sequence. Complete proteome sequence coverage would allow comprehensive characterization of RNA splicing variants and all posttranslational modifications, which would drastically improve the accuracy of biological models. There are many reasons for the sequence coverage deficit, but ultimately peptide length determines sequence observability. Peptides that are too short are lost because they match many protein sequences and their true origin is ambiguous. The maximum observable peptide length is determined by several analytical challenges. This paper explores computationally how peptide lengths produced from several common proteome digestion methods limit observable proteome coverage. Iterative proteome cleavage strategies are also explored. These simulations reveal that maximized proteome coverage can be achieved by use of an iterative digestion protocol involving multiple proteases and chemical cleavages that theoretically allow 92.9% proteome coverage.

scholarly journals Deep conservation of bivalve nacre proteins highlighted by shell matrix proteomics of the Unionoida Elliptio complanata and Villosa lienosa

2017 ◽  
Vol 14 (126) ◽  
pp. 20160846 ◽  
Author(s):  
Benjamin Marie ◽  
Jaison Arivalagan ◽  
Lucrèce Mathéron ◽  
Gérard Bolbach ◽  
Sophie Berland ◽  
...  
Keyword(s):  
Molecular Level ◽  
Complex Mixture ◽  
Pearl Oyster ◽  
Mineral Phase ◽  
Elliptio Complanata ◽  
Proteomic Approach ◽  
Shell Matrix ◽  
Proteomic Study ◽  
Shell Forming

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).

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 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 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.

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
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