Genetic basis for the evolution of vertebrate mineralized tissue

Abstract

Mineralized tissue is vital to many characteristic adaptive phenotypes in vertebrates. Three primary tissues, enamel (enameloid), dentin, and bone, are found in the body armor of ancient agnathans and mammalian teeth, suggesting that these two organs are homologous. Mammalian enamel forms on enamel-specific proteins such as amelogenin, whereas dentin and bone form on collagen and many acidic proteins, such as SPP1, coordinately regulate their mineralization. We previously reported that genes for three major enamel matrix proteins, five proteins necessary for dentin and bone formation, and milk caseins and salivary proteins arose from a single ancestor by tandem gene duplications and form the secretory calcium-binding phosphoprotein (SCPP) family. Gene structure and protein characteristics show that SCPP genes arose from the 5' region of ancestral sparcl1 (SPARC-like 1). Phylogenetic analysis on SPARC and SPARCL1 suggests that the SCPP genes arose after the divergence of cartilaginous fish and bony fish, implying that early vertebrate mineralization did not use SCPPs and that SPARC may be critical for initial mineralization. Consistent with this inference, we identified SPP1 in a teleost genome but failed to find any genes orthologous to mammalian enamel proteins. Based on these observations, we suggest a scenario for the evolution of vertebrate tissue mineralization, in which body armor initially formed on dermal collagen, which acted as a reinforcement of dermis. We also suggest that mammalian enamel is distinct from fish enameloid. Their similar nature as a hard structural overlay on exoskeleton and teeth is because of convergent evolution.

Fig. 1.

Phylogeny and SPARC, SPARCL1, and SCPP gene-duplication history. Symbols for SPARC, SPARCL1, and SCPP genes for dentin/bone, enamel, and casein/saliva are specified in the legend box. The genes for dentin/bone SCPPs, SPARCL1, enamel SCPPs (AMBN and ENAM), and casein/saliva SCPPs are linked on human chromosome 4 in this order (9). No dentin/bone SCPP genes, including SPP1, have been found in fugu or medaka. The scale and phylogeny are based on previous publications (4, 34) and Fig. 4. Dashed lines show extinct agnathan branches.

Fig. 2.

Structures of SPARCL1 (A), SPARC (B), and SPP1 (C). Boxes represent the untranslated region (white), signal peptide (localizes the protein in ECM; gray), and the mature protein (black). The length (nucleotide) of each exon is shown in the boxes. Intron phases are described below. Dashed lines show equivalent introns shifted by intron gain, loss, or sliding. (A) Exons 2–5 code domain I, which is separated by phase 0 introns. Exons 6 and 7 code domain II, and exons 8–11 code domain III. (B) Intron 4 in Ciona and intron 5 in nematode slide 1 base upward or downward, respectively. (C) The penultimate exon codes an Arg-Gly-Asp motif.

Fig. 3.

Evolution of SPARC, SPARCL1, and SPP1. Boxes represent domains I (white), II (black), and III (gray) of SPARC and SPARCL1. SPP1 (white box) arose from domain I of SPARCL1. The length of each box is proportionate to that of each domain. Major amino acids appearing in acidic clusters in domain I are represented as E (Glu), D (Asp), or pS (SXE). The scale and the divergence dates of extant animal taxa are based on Fig. 4.

Fig. 4.

Linearized phylogenetic tree for SPARC and SPARCL1. Figures at the nodes show divergence time based on PC distance, γ distance, and their average from the top. The γ parameter was estimated: α = 1.20. Standard errors are shown for the divergence of SPARC and SPARCL1. The calibration point was set 1,177 mya at the divergence of nematodes and chordates.