Identification and characterization of ameloblastin gene in an amphibian, Xenopus laevis

Population Structure and Selection Signatures in Chinese Indigenous Zhaotong Pigs Revealed by Whole-Genome Resequencing

Zhaotong pig (ZTP) is a Chinese indigenous pig breed in Yunnan Province, known for its unique body shape and appearance, good meat quality, strong foraging ability, and adaptability. However, there is still a lack of research on its genome. In order to investigate the genetic diversity, population structure, and selection signatures of the breed, we conducted a comprehensive analysis by resequencing on 30 ZTPs and comparing them with genomic data from 10 Asian wild boars (AWBs). A total of 45,514,452 autosomal SNPs were detected in the 40 pigs, and 23,649,650 SNPs were retained for further analysis after filtering. The HE, HO, PN, MAF, π, and Fis values were calculated to evaluate the genetic diversity, and the results showed that ZTPs had higher genetic diversity and lower inbreeding coefficient compared with AWBs. Population structure was analyzed using NJ tree, PCA, ADMIXTURE, and LD methods. It was found that ZTPs were population independent of AWBs and had a lower LD decay compared to AWBs. Moreover, the results of the IBS genetic distance and G matrix showed that most of the individuals had large genetic distances and distant genetic relationships in ZTPs. Selection signatures were detected between ZTPs and AWBs by using two methods, FST and π ratio. Totals of 1104 selected regions and 275 candidate genes were identified. Finally, functional enrichment analysis identified some annotated genes that might affect fat deposition (NPY1R, NPY5R, and NMU), reproduction (COL3A1, COL5A2, GLRB, TAC3, and MAP3K12), growth (STAT6 and SQOR), tooth development (AMBN, ENAM, and ODAM), and immune response (MBL2, IL1A, and DNAJA3). Our results will provide a valuable basis for the future effective protection, breeding, and utilization of ZTPs.

Comparative expression of the four enamel matrix protein genes, amelogenin, ameloblastin, enamelin and amelotin during amelogenesis in the lizard Anolis carolinensis

Background

In a recent study, we have demonstrated that amelotin (AMTN) gene structure and its expression during amelogenesis have changed during tetrapod evolution. Indeed, this gene is expressed throughout enamel matrix deposition and maturation in non-mammalian tetrapods, while in mammals its expression is restricted to the transition and maturation stages of amelogenesis. Previous studies of amelogenin (AMEL) gene expression in a lizard and a salamander have shown similar expression pattern to that in mammals, but to our knowledge there are no data regarding ameloblastin (AMBN) and enamelin (ENAM) expression in non-mammalian tetrapods. The present study aims to look at, and compare, the structure and expression of four enamel matrix protein genes, AMEL, AMBN, ENAM and AMTN during amelogenesis in the lizard Anolis carolinensis.

Results

We provide the full-length cDNA sequence of A. carolinensisAMEL and AMBN, and show for the first time the expression of ENAM and AMBN in a non-mammalian species. During amelogenesis in A. carolinensis, AMEL, AMBN and ENAM expression in ameloblasts is similar to that described in mammals. It is noteworthy that AMEL and AMBN expression is also found in odontoblasts.

Conclusions

Our findings indicate that AMTN is the only enamel matrix protein gene that is differentially expressed in ameloblasts between mammals and sauropsids. Changes in AMTN structure and expression could be the key to explain the structural differences between mammalian and reptilian enamel, i.e. prismatic versus non-prismatic.

Evolutionary analysis of selective constraints identifies ameloblastin (AMBN) as a potential candidate for amelogenesis imperfecta

Background

Ameloblastin (AMBN) is a phosphorylated, proline/glutamine-rich protein secreted during enamel formation. Previous studies have revealed that this enamel matrix protein was present early in vertebrate evolution and certainly plays important roles during enamel formation although its precise functions remain unclear. We performed evolutionary analyses of AMBN in order to (i) identify residues and motifs important for the protein function, (ii) predict mutations responsible for genetic diseases, and (iii) understand its molecular evolution in mammals.

Results

In silico searches retrieved 56 complete sequences in public databases that were aligned and analyzed computationally. We showed that AMBN is globally evolving under moderate purifying selection in mammals and contains a strong phylogenetic signal. In addition, our analyses revealed codons evolving under significant positive selection. Evidence for positive selection acting on AMBN was observed in catarrhine primates and the aye-aye. We also found that (i) an additional translation initiation site was recruited in the ancestral placental AMBN, (ii) a short exon was duplicated several times in various species including catarrhine primates, and (iii) several polyadenylation sites are present.

Conclusions

AMBN possesses many positions, which have been subjected to strong selective pressure for 200 million years. These positions correspond to several cleavage sites and hydroxylated, O-glycosylated, and phosphorylated residues. We predict that these conserved positions would be potentially responsible for enamel disorder if substituted. Some motifs that were previously identified as potentially important functionally were confirmed, and we found two, highly conserved, new motifs, the function of which should be tested in the near future. This study illustrates the power of evolutionary analyses for characterizing the functional constraints acting on proteins with yet uncharacterized structure.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0431-0) contains supplementary material, which is available to authorized users.

SCPP genes in the coelacanth: tissue mineralization genes shared by sarcopterygians

The coelacanth is the basal-most extant sarcopterygian that has teeth and tooth-like structures, comprising bone, dentin, and enamel or enameloid. Formation of these tissues involves many members of the secretory calcium-binding protein (SCPP) family. In tetrapods, acidic-residue-rich SCPPs are used in mineralization of bone and dentin, whereas Pro/Gln-rich SCPPs participate in enamel formation. Teleosts also employ many SCPPs for tissue mineralization. Nevertheless, the repertoire of SCPPs is largely different in teleosts and tetrapods; hence, filling this gap would be critical to elucidate early evolution of mineralized tissues in osteichthyans. In the present study, we searched for SCPP genes in the coelacanth genome and identified 11, of which two have clear orthologs in both tetrapods and teleosts, seven only in tetrapods, and two in neither of them. Given the divergence times of these vertebrate lineages, our discovery of this many SCPP genes shared between the coelacanth and tetrapods, but not with teleosts, suggests a complicated evolutionary scheme of SCPP genes in early osteichthyans. Our investigation also revealed both conserved and derived characteristics of SCPPs in the coelacanth and other vertebrates. Notably, acidic SCPPs independently evolved various acidic repeats in different lineages, while maintaining high acidity, presumably important for interactions with calcium. Furthermore, the three Pro/Gln-rich SCPP genes, required for mineralizing enamel matrix and confirmed only in tetrapods, were all identified in the coelacanth, strongly suggesting that enamel is equivalent in the coelacanth and tetrapods. This finding corroborates the previous proposition that true enamel evolved much earlier than the origin of tetrapods.

Amelotin: an enamel matrix protein that experienced distinct evolutionary histories in amphibians, sauropsids and mammals

Background

Amelotin (AMTN) is an ameloblast-secreted protein that belongs to the secretory calcium-binding phosphoprotein (SCPP) family, which originated in early vertebrates. In rodents, AMTN is expressed during the maturation stage of amelogenesis only. This expression pattern strongly differs from the spatiotemporal expression of other ameloblast-secreted SCPPs, such as the enamel matrix proteins (EMPs). Furthermore, AMTN was characterized in rodents only. In this study, we applied various approaches, including in silico screening of databases, PCRs and transcriptome sequencing to characterize AMTN sequences in sauropsids and amphibians, and compared them to available mammalian and coelacanth sequences.

Results

We showed that (i) AMTN is tooth (enamel) specific and underwent pseudogenization in toothless turtles and birds, and (ii) the AMTN structure changed during tetrapod evolution. To infer AMTN function, we studied spatiotemporal expression of AMTN during amelogenesis in a salamander and a lizard, and compared the results with available expression data from mouse. We found that AMTN is expressed throughout amelogenesis in non-mammalian tetrapods, in contrast to its expression limited to enamel maturation in rodents.

Conclusions

Taken together our findings suggest that AMTN was primarily an EMP. Its functions were conserved in amphibians and sauropsids while a change occurred early in the mammalian lineage, modifying its expression pattern during amelogenesis and its gene structure. These changes likely led to a partial loss of AMTN function and could have a link with the emergence of prismatic enamel in mammals.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0329-x) contains supplementary material, which is available to authorized users.

The SCPP gene repertoire in bony vertebrates and graded differences in mineralized tissues

The vertebrate tooth is covered with enamel in most sarcopterygians or enameloid in chondrichthyans and actinopterygians. The evolutionary relationship among these two tissues, the hardest tissue in the body, and other mineralized tissues has long been controversial. We have recently reported that specific combinations of secretory calcium-binding phosphoprotein (SCPP) genes are involved in the mineralization of bone, dentin, enameloid, and enamel. Thus, the early repertoire of SCPP genes would elucidate the evolutionary relationship across these tissues. However, the diversity of SCPP genes in teleosts and tetrapods and the roles of these genes in distinct tissues have remained unclear, mainly because many SCPP genes are lineage-specific. In this study, I show that the repertoire of SCPP genes in the zebrafish, frog, and humans includes many lineage-specific genes and some widely conserved genes that originated in stem osteichthyans or earlier. Expression analysis demonstrates that some frog and zebrafish SCPP genes are used primarily in bone, but also in dentin, while the reverse is true of other genes, similar to some mammalian SCPP genes. Dentin and enameloid initially use shared genes in the matrix, but enameloid is subsequently hypermineralized. Notably, enameloid and enamel use an orthologous SCPP gene in the hypermineralization process. Thus, the hypermineralization machinery ancestral to both enameloid and enamel arose before the actinopterygian-sarcopterygian divergence. However, enamel employs specialized SCPPs as structuring proteins, not used in enameloid, reflecting the divergence of enamel from enameloid. These results show graded differences in mineralized dental tissues and reinforce the hypothesis that bone-dentin-enameloid-enamel constitutes an evolutionary continuum.

Identification and characterization of integrin-binding sialoprotein (IBSP) genes in reptile and amphibian

Integrin-binding sialoprotein (IBSP) is a member of the small integrin-binding ligand N-linked glycoprotein (SIBLING) family; and the whole SIBLING family is further included in a larger secretory calcium-binding phosphoprotein (SCPP) family. SIBLING proteins are known to construct a part of the non-collagenous extracellular matrices of calcified tissues, and considered to have arisen by duplication and subsequent divergent evolution of a single ancient gene. To understand the alterations of SIBLING molecules associated with the evolution of calcified tissues in vertebrates, we initiated a search for lower vertebrate orthologs of SIBLING genes. In the present study, an IBSP ortholog from a reptile (caiman) and two distinct orthologs from an amphibian (African clawed toad) were identified and characterized. As expected, the toad IBSP genes were transcribed only in calcified tissue (jaw and tibia), as also seen in mammals. The caiman, toad, avian, and mammalian IBSPs share several unique features specific for IBSP and apparently have similar properties. Furthermore, analysis of the sequences suggested that the IBSP molecule might have gradually intensified its functions related to calcification during its evolutionary process through tetrapods.

Splicing determines the glycosylation state of ameloblastin

In developing porcine enamel, the space between enamel rods selectively binds lectins and ameloblastin (Ambn) N-terminal antibodies. We tested the hypothesis that ameloblastin N-terminal cleavage products are glycosylated. Assorted Ambn cleavage products showed positive lectin staining by peanut agglutinin (PNA), Maclura pomifera agglutinin (MPA), and Limulus polyphemus agglutinin (LPA), suggesting the presence of an O-linked glycosylation containing galactose (Gal), N-acetylgalactosamine (GalNAc), and sialic acid. Edman sequencing of the lectin-positive bands gave the Ambn N-terminal sequence: VPAFPRQPGTXGVASLXLE. The blank cycles for Pro(11) and Ser(17) confirmed that these residues are hydroxylated and phosphorylated, respectively. The O-glycosylation site was determined by Edman sequencing of pronase-digested Ambn, which gave HPPPLPXQPS, indicating that Ser(86) is the site of the O-linked glycosylation. This modification is within the 15-amino-acid segment (73-YEYSLPVHPPPLPSQ-87) deleted by splicing in the mRNA encoding the 380-amino-acid Ambn isoform. We conclude that only the N-terminal Ambn products derived from the 395-Ambn isoform are glycosylated.

Gene Duplication and the Evolution of Vertebrate Skeletal Mineralization

The mineralized skeleton is a critical innovation that evolved early in vertebrate history. The tissues found in dermal skeletons of ancient vertebrates are similar to the dental tissues of modern vertebrates; both consist of a highly mineralized surface hard tissue, enamel or enameloid, more resilient body dentin, and basal bone. Many proteins regulating mineralization of these tissues are evolutionarily related and form the secretory calcium-binding phosphoprotein (SCPP) family. We hypothesize here the duplication histories of SCPP genes and their common ancestors, SPARC and SPARCL1. At around the same time that Paleozoic jawless vertebrates first evolved mineralized skeleton, SPARCL1 arose from SPARC by whole genome duplication. Then both before and after the split of ray-finned fish and lobe-finned fish, tandem gene duplication created two types of SCPP genes, each residing on the opposite side of SPARCL1. One type was subsequently used in surface tissue and the other in body tissue. In tetrapods, these two types of SCPP genes were separated by intrachromosomal rearrangement. While new SCPP genes arose by duplication, some old genes were eliminated from the genome. As a consequence, phenogenetic drift occurred: while mineralized skeleton is maintained by natural selection, the underlying genetic basis has changed.

The Origin and Evolution of Enamel Mineralization Genes

BACKGROUND/AIMS

Enamel and enameloid were identified in early jawless vertebrates, about 500 million years ago (MYA). This suggests that enamel matrix proteins (EMPs) have at least the same age. We review the current data on the origin, evolution and relationships of enamel mineralization genes.

METHODS AND RESULTS

Three EMPs are secreted by ameloblasts during enamel formation: amelogenin (AMEL), ameloblastin (AMBN) and enamelin (ENAM). Recently, two new genes, amelotin (AMTN) and odontogenic ameloblast associated (ODAM), were found to be expressed by ameloblasts during maturation, increasing the group of ameloblast-secreted proteins to five members. The evolutionary analysis of these five genes indicates that they are related: AMEL is derived from AMBN, AMTN and ODAM are sister genes, and all are derived from ENAM. Using molecular dating, we showed that AMBN/AMEL duplication occurred >600 MYA. The large sequence dataset available for mammals and reptiles was used to study AMEL evolution. In the N- and C-terminal regions, numerous residues were unchanged during >200 million years, suggesting that they are important for the proper function of the protein.

CONCLUSION

The evolutionary analysis of AMEL led to propose a dataset that will be useful to validate AMEL mutations leading to X- linked AI.

Identification and characterization of matrix metalloproteinase-20 (MMP20; enamelysin) genes in reptile and amphibian

Matrix metalloproteinase-20 (MMP20; enamelysin) is important for proteolytic processing of extracellular matrix (ECM) proteins during the formation of enamel and plays a critical role in proteolytic processing of amelogenin (AMEL), the most abundant enamel ECM protein. MMP20 might have played a role in the emergence of teeth, because jawless vertebrates with primordial teeth on their external skeletons may have possessed the MMP20 gene, and MMP20 and enamel ECM proteins are thought to have evolved together in a special relationship over time. Thus, an understanding of the molecular evolution of the MMP20 gene is important for elucidating the evolution of enamel and it is necessary to identify the orthologs of the MMP20 gene in non-mammals, as it has been identified in mammals. In the present study, orthologs of the MMP20 genes from a reptile (caiman) and an amphibian (African clawed toad) were cloned and characterized. Comparisons of the orthologs revealed that the MMP20 proteins were highly conserved throughout the evolution of tetrapods. Further, the caiman, toad, and mammalian MMP20 shared several unique features specific for MMP20, but not for other matrix metalloproteinases. In addition, the toad MMP20 gene was transcribed only in the upper jaw, presumably in teeth. These results suggest that MMP20 in a common ancestor of tetrapods might have been recruited for the processing of AMEL and conserved over 350 million years of evolution.

Expression of ameloblastin during enamel formation in a crocodile

Ameloblastin is an enamel-specific protein that plays critical roles in enamel formation, as well as adhesion between ameloblasts and the enamel matrix, as shown by analyses of ameloblastin-null mice. In the present study, we produced two distinct antibodies that recognize the N-terminus and C-terminus regions of caiman ameloblastin, in order to elucidate the fate of ameloblastin peptides during tooth development. An immunohistochemical study using the antibodies showed that caiman ameloblastin was a tooth-specific matrix protein that may initially be cleaved into two groups, N- and C-terminal peptides, as shown in mammals. The distribution of the N-terminal peptides was much different from that of the C-terminal peptides during enamel formation; however, it was similar to that of mammalian ameloblastin. Although ameloblastin is thought to have a relationship with the enamel prismatic structure in mammals, in the caiman, which has non-prismatic enamel, functional ameloblastin has no relationship with any enamel structure. Consequently, it is suggested that ameloblastin has kept its original functions during the evolutionary transition from reptiles to mammals and that it has been conserved in both lineages during more than 200 million years of evolution. Our results support the notion that ameloblastin acts as a factor for ameloblast adhesion to enamel matrix, because distribution of the C-terminal peptides was consistently restricted on the surface layers of enamel matrix specimens ranging from immature to nearly completely mature. The principal molecules that provide the adhesive function are presumably C-terminal peptides.

Phenogenetic drift in evolution: the changing genetic basis of vertebrate teeth

Vertebrate mineralized tissues are vital to the adaptive evolution of various traits. Among these traits is the tooth, which consists of two characteristic mineralized tissues, a highly mineralized surface layer (enamel in tetrapods and enameloid in fish) and a softer body (dentin), both supported by basal bone. However, enamel and enameloid are significantly different in development, and dentin shows many histological variations; hence their evolution has been intensively studied. Nevertheless, their genetic basis has been revealed only in tetrapods. We previously reported that many genes involved in tetrapod tissue mineralization arose from a common ancestor and constitute the secretory calcium-binding phosphoprotein (SCPP) gene family. Now we show that teleost fish also use many SCPPs for enameloid and dentin mineralization, but none of these directly corresponds to tetrapod SCPPs. This finding suggests that teleost and tetrapod SCPP genes have experienced independent parallel duplication histories. Thus, through phenogenetic drift, the tooth has remained a stable trait in jawed vertebrates, while evolving distinct genetic bases in teleosts and tetrapods. The characteristics of teleost SCPP genes and their expression domains in tooth development suggest the possibility that enameloid arose from dentin and enamel from enameloid more than once in vertebrate evolution. In fugu (puffer fish), expression of SCPP genes is also detected in an unusual beak-like structure that shelters numerous teeth. Their expression pattern suggests that the jaw consists of the dentin beak and supportive bone. These findings illustrate the complexity of the homology concept in understanding evolution, particularly the evolution of mineralized tissues.

Genetic basis for the evolution of vertebrate mineralized tissue

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.