In-depth, high-accuracy proteomics of sea urchin tooth organic matrix

Abstract

Background: The organic matrix contained in biominerals plays an important role in regulating mineralization and in determining biomineral properties. However, most components of biomineral matrices remain unknown at present. In sea urchin tooth, which is an important model for developmental biology and biomineralization, only few matrix components have been identified. The recent publication of the Strongylocentrotus purpuratus genome sequence rendered possible not only the identification of genes potentially coding for matrix proteins, but also the direct identification of proteins contained in matrices of skeletal elements by in-depth, high-accuracy proteomic analysis.

Results: We identified 138 proteins in the matrix of tooth powder. Only 56 of these proteins were previously identified in the matrices of test (shell) and spine. Among the novel components was an interesting group of five proteins containing alanine- and proline-rich neutral or basic motifs separated by acidic glycine-rich motifs. In addition, four of the five proteins contained either one or two predicted Kazal protease inhibitor domains. The major components of tooth matrix were however largely identical to the set of spicule matrix proteins and MSP130-related proteins identified in test (shell) and spine matrix. Comparison of the matrices of crushed teeth to intact teeth revealed a marked dilution of known intracrystalline matrix proteins and a concomitant increase in some intracellular proteins.

Conclusion: This report presents the most comprehensive list of sea urchin tooth matrix proteins available at present. The complex mixture of proteins identified may reflect many different aspects of the mineralization process. A comparison between intact tooth matrix, presumably containing odontoblast remnants, and crushed tooth matrix served to differentiate between matrix components and possible contributions of cellular remnants. Because LC-MS/MS-based methods directly measures peptides our results validate many predicted genes and confirm the existence of the corresponding proteins. Knowledge of the components of this model system may stimulate further experiments aiming at the elucidation of structure, function, and interaction of biomineral matrix components.

Figure 1

SDS-PAGE separation of tooth powder organic matrix proteins. The mass of marker proteins is shown in kDa to the left. Approximately 200 μg of matrix were applied per lane. Sections excised for in-gel digestion are indicated to the right.

Figure 2

Analysis of the AP-rich protein contained in entry Glean3:17589. The predicted signal peptide is in bold and underlined. The predicted Kazal domain is shaded blue. Yellow and grey shading indicate Ala/Pro-rich motifs and acidic sequence regions, respectively. Peptides identified by MS/MS are in red.

Figure 3

Alignment of Glean3:15124 to selected selenoprotein M sequences. Amino acids conserved in three of the four sequences are in boxes. The numbering of sequence positions corresponds to the numbering in precursor proteins. The sequences are from UniProtKB/TrEMBL entries A5J2A1_PENVA (Litopenaeus vannamei), SELM_DANRE (Zebrafish, primary accession number Q802G7), and SELM_MOUSE (primary accession number Q8VHC3). Peptides sequenced by MS/MS are shown in red.