Biomineralization toolkit: The importance of sample cleaning prior to the characterization of biomineral proteomes

Ramos-Silva, Paula; Marin, Frédéric; Kaandorp, Jaap A.; Marie, Benjamin

doi:10.1073/pnas.1303657110

Cited by 33 publications

(45 citation statements)

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“…More recently, two proteomic studies of the organic matrix of adult coral skeletons Ramos-Silva et al 2013a) have provided a large set of new candidates for involvement in calcification. However, while many of the same proteins were identified in both studies, some of the components reported by Drake et al (2013) were almost certainly cellular contaminants rather than true skeletal components (Ramos-Silva et al 2013b). More recently still, some of the proteins described by Drake et al (2013) have been characterized further and localized (e.g.…”

Section: Introductionmentioning

confidence: 78%

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Transcriptomic differences between day and night in Acropora millepora provide new insights into metabolite exchange and light‐enhanced calcification in corals

et al. 2015

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The evolutionary success of reef-building corals is often attributed to their symbiotic relationship with photosynthetic dinoflagellates of the genus Symbiodinium, but metabolic interactions between the partners and the molecular bases of light-enhanced calcification (LEC) are not well understood. Here, the metabolic bases of the interaction between the coral Acropora millepora and its dinoflagellate symbiont were investigated by comparing gene expression levels under light and dark conditions at the whole transcriptome level. Among the 497 differentially expressed genes identified, a suite of genes involved in cholesterol transport was found to be upregulated under light conditions, confirming the significance of this compound in the coral symbiosis. Although ion transporters likely to have roles in calcification were not differentially expressed in this study, expression levels of many genes associated with skeletal organic matrix composition and organization were higher in light conditions. This implies that the rate of organic matrix synthesis is one factor limiting calcification at night. Thus, LEC during the day is likely to be a consequence of increases in both matrix synthesis and the supply of precursor molecules as a result of photosynthetic activity.

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Section: Introductionmentioning

confidence: 78%

“…() were almost certainly cellular contaminants rather than true skeletal components (Ramos‐Silva et al . ). More recently still, some of the proteins described by Drake et al .…”

Section: Introductionmentioning

confidence: 97%

Transcriptomic differences between day and night in Acropora millepora provide new insights into metabolite exchange and light‐enhanced calcification in corals

et al. 2015

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“…2). Although the proteomic analyses of the “first batch” revealed intracellular coral proteins and proteins of symbiont origin (Ramos-Silva et al 2013), the second batch was free of such contaminants, enabling the detection of 43 unique A. millepora proteins likely to constitute the SOMP repertoire, that is, proteins that are strongly associated to the skeleton. Of these 43 proteins, 36 assignments could be made with high confidence (i.e., with more than one unique peptide matching the sequence, supplementary table S1, Supplementary Material online), whereas seven sequences each with only a single peptide match were dropped from the list (supplementary table S2, Supplementary Material online) despite their properties being generally consistent with those of the high-confidence data set.…”

Section: Resultsmentioning

confidence: 99%

The Skeletal Proteome of the Coral Acropora millepora: The Evolution of Calcification by Co-Option and Domain Shuffling

Ramos-Silva

Kaandorp

Huisman

et al. 2013

Molecular Biology and Evolution

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168

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In corals, biocalcification is a major function that may be drastically affected by ocean acidification (OA). Scleractinian corals grow by building up aragonitic exoskeletons that provide support and protection for soft tissues. Although this process has been extensively studied, the molecular basis of biocalcification is poorly understood. Notably lacking is a comprehensive catalog of the skeleton-occluded proteins—the skeletal organic matrix proteins (SOMPs) that are thought to regulate the mineral deposition. Using a combination of proteomics and transcriptomics, we report the first survey of such proteins in the staghorn coral Acropora millepora. The organic matrix (OM) extracted from the coral skeleton was analyzed by mass spectrometry and bioinformatics, enabling the identification of 36 SOMPs. These results provide novel insights into the molecular basis of coral calcification and the macroevolution of metazoan calcifying systems, whereas establishing a platform for studying the impact of OA at molecular level. Besides secreted proteins, extracellular regions of transmembrane proteins are also present, suggesting a close control of aragonite deposition by the calicoblastic epithelium. In addition to the expected SOMPs (Asp/Glu-rich, galaxins), the skeletal repertoire included several proteins containing known extracellular matrix domains. From an evolutionary perspective, the number of coral-specific proteins is low, many SOMPs having counterparts in the noncalcifying cnidarians. Extending the comparison with the skeletal OM proteomes of other metazoans allowed the identification of a pool of functional domains shared between phyla. These data suggest that co-option and domain shuffling may be general mechanisms by which the trait of calcification has evolved.

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“…Because the surface of the coral skeleton can be easily contaminated by extraneous N, the cleaning process is critical for removing any contaminant N on the surfaces of the skeleton powder (Ramos-Silva et al, 2013). To characterize the effect of the cleaning, we compared the NaOCl cleaning protocol with an analogous persulfate-based cleaning used for foraminifera-bound N isotope analyses (Ren et al, 2012) and with no cleaning.…”

Section: Methods Validationmentioning

confidence: 99%

Isotopic composition of skeleton-bound organic nitrogen in reef-building symbiotic corals: A new method and proxy evaluation at Bermuda

Wang

Sigman

Cohen

et al. 2015

Geochimica et Cosmochimica Acta

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Biomineralization toolkit: The importance of sample cleaning prior to the characterization of biomineral proteomes

Cited by 33 publications

References 4 publications

Transcriptomic differences between day and night in Acropora millepora provide new insights into metabolite exchange and light‐enhanced calcification in corals

Transcriptomic differences between day and night in Acropora millepora provide new insights into metabolite exchange and light‐enhanced calcification in corals

The Skeletal Proteome of the Coral Acropora millepora: The Evolution of Calcification by Co-Option and Domain Shuffling

Isotopic composition of skeleton-bound organic nitrogen in reef-building symbiotic corals: A new method and proxy evaluation at Bermuda

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