Click
here to close Hello! We notice that
you are using Internet Explorer, which is not supported by Echinobase
and may cause the site to display incorrectly. We suggest using a
current version of Chrome,
FireFox,
or Safari.
Proteome Sci
2008 Dec 09;6:33. doi: 10.1186/1477-5956-6-33.
Show Gene links
Show Anatomy links
In-depth, high-accuracy proteomics of sea urchin tooth organic matrix.
Mann K
,
Poustka AJ
,
Mann M
.
???displayArticle.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.
Alvares,
The proteome of the developing tooth of the sea urchin, Lytechinus variegatus: mortalin is a constituent of the developing cell syncytium.
2007, Pubmed,
Echinobase
Alvares,
The proteome of the developing tooth of the sea urchin, Lytechinus variegatus: mortalin is a constituent of the developing cell syncytium.
2007,
Pubmed
,
Echinobase
Ameye,
Ultrastructural localization of proteins involved in sea urchin biomineralization.
1999,
Pubmed
,
Echinobase
Amore,
cis-Regulatory control of cyclophilin, a member of the ETS-DRI skeletogenic gene battery in the sea urchin embryo.
2006,
Pubmed
,
Echinobase
Ansong,
Proteogenomics: needs and roles to be filled by proteomics in genome annotation.
2008,
Pubmed
Benson,
A lineage-specific gene encoding a major matrix protein of the sea urchin embryo spicule. I. Authentication of the cloned gene and its developmental expression.
1987,
Pubmed
,
Echinobase
Berman,
Intercalation of sea urchin proteins in calcite: study of a crystalline composite material.
1990,
Pubmed
,
Echinobase
Cheers,
P16 is an essential regulator of skeletogenesis in the sea urchin embryo.
2005,
Pubmed
,
Echinobase
George,
Characterization and expression of a gene encoding a 30.6-kDa Strongylocentrotus purpuratus spicule matrix protein.
1991,
Pubmed
,
Echinobase
Gupta,
Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes.
2008,
Pubmed
Illies,
Identification and developmental expression of new biomineralization proteins in the sea urchin Strongylocentrotus purpuratus.
2002,
Pubmed
,
Echinobase
Ingersoll,
Ultrastructural localization of spicule matrix proteins in normal and metalloproteinase inhibitor-treated sea urchin primary mesenchyme cells.
2003,
Pubmed
,
Echinobase
Ingersoll,
Matrix metalloproteinase inhibitors disrupt spicule formation by primary mesenchyme cells in the sea urchin embryo.
1998,
Pubmed
,
Echinobase
Ishihama,
Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein.
2005,
Pubmed
Kapłon,
Starmaker exhibits properties of an intrinsically disordered protein.
2008,
Pubmed
Klein,
The low molecular weight proteome of Halobacterium salinarum.
2007,
Pubmed
Kniprath,
Ultrastructure and growth of the sea urchin tooth.
1974,
Pubmed
,
Echinobase
Livingston,
A genome-wide analysis of biomineralization-related proteins in the sea urchin Strongylocentrotus purpuratus.
2006,
Pubmed
,
Echinobase
Mann,
The sea urchin (Strongylocentrotus purpuratus) test and spine proteomes.
2008,
Pubmed
,
Echinobase
Mann,
Proteomic analysis of the acid-soluble organic matrix of the chicken calcified eggshell layer.
2006,
Pubmed
Marchler-Bauer,
CD-Search: protein domain annotations on the fly.
2004,
Pubmed
Olsen,
Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap.
2005,
Pubmed
Olsen,
Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation.
2004,
Pubmed
Parseghian,
Beyond the walls of the nucleus: the role of histones in cellular signaling and innate immunity.
2006,
Pubmed
Poustka,
A global view of gene expression in lithium and zinc treated sea urchin embryos: new components of gene regulatory networks.
2007,
Pubmed
,
Echinobase
Rappsilber,
Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics.
2003,
Pubmed
Roe,
Inhibitors of metalloendoproteases block spiculogenesis in sea urchin primary mesenchyme cells.
1989,
Pubmed
,
Echinobase
Shevchenko,
In-gel digestion for mass spectrometric characterization of proteins and proteomes.
2006,
Pubmed
Sodergren,
The genome of the sea urchin Strongylocentrotus purpuratus.
2006,
Pubmed
,
Echinobase
Söllner,
Control of crystal size and lattice formation by starmaker in otolith biomineralization.
2003,
Pubmed
Veis,
Matrix proteins of the teeth of the sea urchin Lytechinus variegatus.
1986,
Pubmed
,
Echinobase
Veis,
Mineral-related proteins of sea urchin teeth: Lytechinus variegatus.
2002,
Pubmed
,
Echinobase
Wang,
Design strategies of sea urchin teeth: structure, composition and micromechanical relations to function.
1997,
Pubmed
,
Echinobase
Weiner,
Organic matrixlike macromolecules associated with the mineral phase of sea urchin skeletal plates and teeth.
1985,
Pubmed
,
Echinobase
Wilt,
The dynamics of secretion during sea urchin embryonic skeleton formation.
2008,
Pubmed
,
Echinobase
Wustman,
Identification of a "glycine-loop"-like coiled structure in the 34 AA Pro,Gly,Met repeat domain of the biomineral-associated protein, PM27.
2002,
Pubmed
,
Echinobase
Zhang,
Model peptide studies of sequence repeats derived from the intracrystalline biomineralization protein, SM50. II. Pro,Asn-rich tandem repeats.
2000,
Pubmed
,
Echinobase
