Fig 1.
List of skeletal organic matrix proteins in A. digitifera.
See also S3 Table. a: The presence of a signal peptide at the N-terminus predicted by SignalP [40]. b: Possible extracellular localization predicted by SecretomeP [41]. c: Presence of a transmembrane domain predicted by TMHMM [42]. d: Phosphorylation detected by MS/MS. e: Orthologous protein in the A. millepora proteome [29]. f: Orthologous protein in the S. pistillata proteome [26].
Fig 2.
Gene expression patterns of SOMPs and SEM images of coral skeletons of polyp and adult stages.
(a) Heatmap of SOMP gene expression at different developmental stages. Three expression patterns are indicated at the left: continuous expression before and during calcification (Pattern 1), strong expression commencing during the planula or polyp stages (Pattern 2), and exclusive expression in adult stage (Pattern 3). The color key represents FPKM of normalized log2 transformed counts. Orange to red color intensity indicates higher gene expression. Polyp and adult stages, in which corals generate calcium carbonate skeletons, are boxed in black. (b, c) SEM images of polyp (b) and adult (c) skeletons. The individual polyp used here was fixed seven days after settlement. Soft tissue of each sample was removed with 10% NaOH. After settlement, the disk-like structure was deposited onto the substrate. Then, a network structure similar to that of an adult skeleton began to form.
Fig 3.
Number of proteins with specific domain architecture encoded in animal genomes.
a: Figures in parentheses indicate number of proteins without transmembrane domain.
Fig 4.
Domain architectures of SOMPs from Acropora digitifera and sea anemone proteins similar to the SOMPs.
(a) Cadherin. (b) Neurexin. (c) REJ domain-containing protein (dcp). (d) Zona pellucida dcp. (e) Multi-copper oxidase. (f) MAM and LDL receptor dcp. (g) TSP-1 and VWA dcp. (h) Mucin4-like protein. (i) CUB dcp. (j) Vitellogenin-like protein. Lengths of amino acid sequences are shown at the right.
Fig 5.
Evolutionary and stepwise acquisition processes for coral skeleton formation.
In Phase I, pre-existing proteins that functioned in cellular activity and developmental processes in non-skeletal cnidarians, may have acquired additional functions, presumably for attachment to the substrate and to constitute the initial extracellular organic matrix. In Phase II, novel proteins emerged after gene duplication, domain shuffling, and rapid molecular evolution, and became specifically involved in constructing the organic matrix framework. Finally, unique proteins emerged in the coral lineage (Phase III). They may have interacted with other organic matrix proteins to play important roles in crystal formation.