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Randall JG, Gatesy J, McGowen MR, Springer MS. Molecular Evidence for Relaxed Selection on the Enamel Genes of Toothed Whales (Odontoceti) with Degenerative Enamel Phenotypes. Genes (Basel) 2024; 15:228. [PMID: 38397217 PMCID: PMC10888366 DOI: 10.3390/genes15020228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Different species of toothed whales (Odontoceti) exhibit a variety of tooth forms and enamel types. Some odontocetes have highly prismatic enamel with Hunter-Schreger bands, whereas enamel is vestigial or entirely lacking in other species. Different tooth forms and enamel types are associated with alternate feeding strategies that range from biting and grasping prey with teeth in most oceanic and river dolphins to the suction feeding of softer prey items without the use of teeth in many beaked whales. At the molecular level, previous studies have documented inactivating mutations in the enamel-specific genes of some odontocete species that lack complex enamel. At a broader scale, however, it is unclear whether enamel complexity across the full diversity of extant Odontoceti correlates with the relative strength of purifying selection on enamel-specific genes. Here, we employ sequence alignments for seven enamel-specific genes (ACP4, AMBN, AMELX, AMTN, ENAM, KLK4, MMP20) in 62 odontocete species that are representative of all extant families. The sequences for 33 odontocete species were obtained from databases, and sequences for the remaining 29 species were newly generated for this study. We screened these alignments for inactivating mutations (e.g., frameshift indels) and provide a comprehensive catalog of these mutations in species with one or more inactivated enamel genes. Inactivating mutations are rare in Delphinidae (oceanic dolphins) and Platanistidae/Inioidea (river dolphins) that have higher enamel complexity scores. By contrast, mutations are much more numerous in clades such as Monodontidae (narwhal, beluga), Ziphiidae (beaked whales), Physeteroidea (sperm whales), and Phocoenidae (porpoises) that are characterized by simpler enamel or even enamelless teeth. Further, several higher-level taxa (e.g., Hyperoodon, Kogiidae, Monodontidae) possess shared inactivating mutations in one or more enamel genes, which suggests loss of function of these genes in the common ancestor of each clade. We also performed selection (dN/dS) analyses on a concatenation of these genes and used linear regression and Spearman's rank-order correlation to test for correlations between enamel complexity and two different measures of selection intensity (# of inactivating mutations per million years, dN/dS values). Selection analyses revealed that relaxed purifying selection is especially prominent in physeteroids, monodontids, and phocoenids. Linear regressions and correlation analyses revealed a strong negative correlation between selective pressure (dN/dS values) and enamel complexity. Stronger purifying selection (low dN/dS) is found on branches with more complex enamel and weaker purifying selection (higher dN/dS) occurs on branches with less complex enamel or enamelless teeth. As odontocetes diversified into a variety of feeding modes, in particular, the suction capture of prey, a reduced reliance on the dentition for prey capture resulted in the relaxed selection of genes that are critical to enamel development.
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Affiliation(s)
- Jason G. Randall
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA;
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA;
| | - Michael R. McGowen
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, MRC 108, P.O. Box 37012, Washington, DC 20013, USA;
| | - Mark S. Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA;
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Early evolution of enamel matrix proteins is reflected by pleiotropy of physiological functions. Sci Rep 2023; 13:1471. [PMID: 36702824 PMCID: PMC9879986 DOI: 10.1038/s41598-023-28388-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
Highly specialized enamel matrix proteins (EMPs) are predominantly expressed in odontogenic tissues and diverged from common ancestral gene. They are crucial for the maturation of enamel and its extreme complexity in multiple independent lineages. However, divergence of EMPs occured already before the true enamel evolved and their conservancy in toothless species suggests that non-canonical functions are still under natural selection. To elucidate this hypothesis, we carried out an unbiased, comprehensive phenotyping and employed data from the International Mouse Phenotyping Consortium to show functional pleiotropy of amelogenin, ameloblastin, amelotin, and enamelin, genes, i.e. in sensory function, skeletal morphology, cardiovascular function, metabolism, immune system screen, behavior, reproduction, and respiratory function. Mice in all KO mutant lines, i.e. amelogenin KO, ameloblastin KO, amelotin KO, and enamelin KO, as well as mice from the lineage with monomeric form of ameloblastin were affected in multiple physiological systems. Evolutionary conserved motifs and functional pleiotropy support the hypothesis of role of EMPs as general physiological regulators. These findings illustrate how their non-canonical function can still effect the fitness of modern species by an example of influence of amelogenin and ameloblastin on the bone physiology.
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Randall JG, Gatesy J, Springer MS. Molecular evolutionary analyses of tooth genes support sequential loss of enamel and teeth in baleen whales (Mysticeti). Mol Phylogenet Evol 2022; 171:107463. [PMID: 35358696 DOI: 10.1016/j.ympev.2022.107463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/16/2021] [Accepted: 03/01/2022] [Indexed: 10/18/2022]
Abstract
The loss of teeth and evolution of baleen racks in Mysticeti was a profound transformation that permitted baleen whales to radiate and diversify into a previously underutilized ecological niche of bulk filter-feeding on zooplankton and other small prey. Ancestral state reconstructions suggest that postnatal teeth were lost in the common ancestor of crown Mysticeti. Genomic studies provide some support for this hypothesis and suggest that the genetic toolkit for enamel production was inactivated in the common ancestor of living baleen whales. However, molecular studies to date have not provided direct evidence for the complete loss of teeth, including their dentin component, on the stem mysticete branch. Given these results, several questions remain unanswered: (1) Were teeth lost in a single step or did enamel loss precede dentin loss? (2) Was enamel lost early or late on the stem mysticete branch? (3) If enamel and dentin/tooth loss were decoupled in the ancestry of baleen whales, did dentin loss occur on the stem mysticete branch or independently in different crown mysticete lineages? To address these outstanding questions, we compiled and analyzed complete protein-coding sequences for nine tooth-related genes from cetaceans with available genome data. Seven of these genes are associated with enamel formation (ACP4, AMBN, AMELX, AMTN, ENAM, KLK4, MMP20) whereas two other genes are either dentin-specific (DSPP) or tooth-specific (ODAPH) but not enamel-specific. Molecular evolutionary analyses indicate that all seven enamel-specific genes have inactivating mutations that are scattered across branches of the mysticete tree. Three of the enamel genes (ACP4, KLK4, MMP20) have inactivating mutations that are shared by all mysticetes. The two genes that are dentin-specific (DSPP) or tooth-specific (ODAPH) do not have any inactivating mutations that are shared by all mysticetes, but there are shared mutations in Balaenidae as well as in Plicogulae (Neobalaenidae + Balaenopteroidea). These shared mutations suggest that teeth were lost at most two times. Shared inactivating mutations and dN/dS analyses, in combination with cetacean divergence times, were used to estimate inactivation times of genes and by proxy enamel and tooth phenotypes at ancestral nodes. The results of these analyses are most compatible with a two-step model for the loss of teeth in the ancestry of living baleen whales: enamel was lost very early on the stem Mysticeti branch followed by the independent loss of dentin (and teeth) in the common ancestors of Balaenidae and Plicogulae, respectively. These results imply that some stem mysticetes, and even early crown mysticetes, may have had vestigial teeth comprised of dentin with no enamel. Our results also demonstrate that all odontocete species (in our study) with absent or degenerative enamel have inactivating mutations in one or more of their enamel genes.
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Affiliation(s)
- Jason G Randall
- Department of Evolution, Ecology, and Evolutionary Biology, University of California, Riverside, CA 92521, USA.
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA.
| | - Mark S Springer
- Department of Evolution, Ecology, and Evolutionary Biology, University of California, Riverside, CA 92521, USA.
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Odontogenesis-associated phosphoprotein truncation blocks ameloblast transition into maturation in Odaph C41*/C41* mice. Sci Rep 2021; 11:1132. [PMID: 33441959 PMCID: PMC7807025 DOI: 10.1038/s41598-020-80912-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/21/2020] [Indexed: 01/29/2023] Open
Abstract
Mutations of Odontogenesis-Associated Phosphoprotein (ODAPH, OMIM *614829) cause autosomal recessive amelogenesis imperfecta, however, the function of ODAPH during amelogenesis is unknown. Here we characterized normal Odaph expression by in situ hybridization, generated Odaph truncation mice using CRISPR/Cas9 to replace the TGC codon encoding Cys41 into a TGA translation termination codon, and characterized and compared molar and incisor tooth formation in Odaph+/+, Odaph+/C41*, and OdaphC41*/C41* mice. We also searched genomes to determine when Odaph first appeared phylogenetically. We determined that tooth development in Odaph+/+ and Odaph+/C41* mice was indistinguishable in all respects, so the condition in mice is inherited in a recessive pattern, as it is in humans. Odaph is specifically expressed by ameloblasts starting with the onset of post-secretory transition and continues until mid-maturation. Based upon histological and ultrastructural analyses, we determined that the secretory stage of amelogenesis is not affected in OdaphC41*/C41* mice. The enamel layer achieves a normal shape and contour, normal thickness, and normal rod decussation. The fundamental problem in OdaphC41*/C41* mice starts during post-secretory transition, which fails to generate maturation stage ameloblasts. At the onset of what should be enamel maturation, a cyst forms that separates flattened ameloblasts from the enamel surface. The maturation stage fails completely.
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Alazem O, Abramyan J. Reptile enamel matrix proteins: Selection, divergence, and functional constraint. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2019; 332:136-148. [PMID: 31045323 DOI: 10.1002/jez.b.22857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 02/24/2019] [Accepted: 04/01/2019] [Indexed: 12/14/2022]
Abstract
The three major enamel matrix proteins (EMPs): amelogenin (AMEL), ameloblastin (AMBN), and enamelin (ENAM), are intrinsically linked to tooth development in tetrapods. However, reptiles and mammals exhibit significant differences in dental patterning and development, potentially affecting how EMPs evolve in each group. In most reptiles, teeth are replaced continuously throughout life, while mammals have reduced replacement to only one or two generations. Reptiles also form structurally simple, aprismatic enamel while mammalian enamel is composed of highly organized hydroxyapatite prisms. These differences, combined with reported low sequence homology in reptiles, led us to predict that reptiles may experience lower selection pressure on their EMPs as compared with mammals. However, we found that like mammals, reptile EMPs are under moderate purifying selection, with some differences evident between AMEL, AMBN, and ENAM. We also demonstrate that sequence homology in reptile EMPs is closely associated with divergence times, with more recently diverged lineages exhibiting high homology, along with strong phylogenetic signal. Lastly, despite sequence divergence, none of the reptile species in our study exhibited mutations consistent with diseases that cause degeneration of enamel (e.g. amelogenesis imperfecta). Despite short tooth retention time and simplicity in enamel structure, reptile EMPs still exhibit purifying selection required to form durable enamel.
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Affiliation(s)
- Omar Alazem
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, Michigan
| | - John Abramyan
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, Michigan
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Brookes SJ, Barron MJ, Dixon MJ, Kirkham J. The Unfolded Protein Response in Amelogenesis and Enamel Pathologies. Front Physiol 2017; 8:653. [PMID: 28951722 PMCID: PMC5599773 DOI: 10.3389/fphys.2017.00653] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/17/2017] [Indexed: 12/18/2022] Open
Abstract
During the secretory phase of their life-cycle, ameloblasts are highly specialized secretory cells whose role is to elaborate an extracellular matrix that ultimately confers both form and function to dental enamel, the most highly mineralized of all mammalian tissues. In common with many other “professional” secretory cells, ameloblasts employ the unfolded protein response (UPR) to help them cope with the large secretory cargo of extracellular matrix proteins transiting their ER (endoplasmic reticulum)/Golgi complex and so minimize ER stress. However, the UPR is a double-edged sword, and, in cases where ER stress is severe and prolonged, the UPR switches from pro-survival to pro-apoptotic mode. The purpose of this review is to consider the role of the ameloblast UPR in the biology and pathology of amelogenesis; specifically in respect of amelogenesis imperfecta (AI) and fluorosis. Some forms of AI appear to correspond to classic proteopathies, where pathological intra-cellular accumulations of protein tip the UPR toward apoptosis. Fluorosis also involves the UPR and, while not of itself a classic proteopathic disease, shares some common elements through the involvement of the UPR. The possibility of therapeutic intervention by pharmacological modulation of the UPR in AI and fluorosis is also discussed.
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Affiliation(s)
- Steven J Brookes
- Division of Oral Biology, School of Dentistry, University of Leeds, St James's University HospitalLeeds, United Kingdom
| | - Martin J Barron
- Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre, University of ManchesterManchester, United Kingdom
| | - Michael J Dixon
- Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre, University of ManchesterManchester, United Kingdom
| | - Jennifer Kirkham
- Division of Oral Biology, School of Dentistry, University of Leeds, St James's University HospitalLeeds, United Kingdom
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Lacruz RS, Habelitz S, Wright JT, Paine ML. DENTAL ENAMEL FORMATION AND IMPLICATIONS FOR ORAL HEALTH AND DISEASE. Physiol Rev 2017; 97:939-993. [PMID: 28468833 DOI: 10.1152/physrev.00030.2016] [Citation(s) in RCA: 223] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 01/10/2017] [Accepted: 01/10/2017] [Indexed: 12/16/2022] Open
Abstract
Dental enamel is the hardest and most mineralized tissue in extinct and extant vertebrate species and provides maximum durability that allows teeth to function as weapons and/or tools as well as for food processing. Enamel development and mineralization is an intricate process tightly regulated by cells of the enamel organ called ameloblasts. These heavily polarized cells form a monolayer around the developing enamel tissue and move as a single forming front in specified directions as they lay down a proteinaceous matrix that serves as a template for crystal growth. Ameloblasts maintain intercellular connections creating a semi-permeable barrier that at one end (basal/proximal) receives nutrients and ions from blood vessels, and at the opposite end (secretory/apical/distal) forms extracellular crystals within specified pH conditions. In this unique environment, ameloblasts orchestrate crystal growth via multiple cellular activities including modulating the transport of minerals and ions, pH regulation, proteolysis, and endocytosis. In many vertebrates, the bulk of the enamel tissue volume is first formed and subsequently mineralized by these same cells as they retransform their morphology and function. Cell death by apoptosis and regression are the fates of many ameloblasts following enamel maturation, and what cells remain of the enamel organ are shed during tooth eruption, or are incorporated into the tooth's epithelial attachment to the oral gingiva. In this review, we examine key aspects of dental enamel formation, from its developmental genesis to the ever-increasing wealth of data on the mechanisms mediating ionic transport, as well as the clinical outcomes resulting from abnormal ameloblast function.
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Affiliation(s)
- Rodrigo S Lacruz
- Department of Basic Science and Craniofacial Biology, College of Dentistry, New York University, New York, New York; Department of Preventive and Restorative Dental Sciences, University of California, San Francisco, San Francisco, California; Department of Pediatric Dentistry, School of Dentistry, University of North Carolina, Chapel Hill, North Carolina; Herman Ostrow School of Dentistry, Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, California
| | - Stefan Habelitz
- Department of Basic Science and Craniofacial Biology, College of Dentistry, New York University, New York, New York; Department of Preventive and Restorative Dental Sciences, University of California, San Francisco, San Francisco, California; Department of Pediatric Dentistry, School of Dentistry, University of North Carolina, Chapel Hill, North Carolina; Herman Ostrow School of Dentistry, Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, California
| | - J Timothy Wright
- Department of Basic Science and Craniofacial Biology, College of Dentistry, New York University, New York, New York; Department of Preventive and Restorative Dental Sciences, University of California, San Francisco, San Francisco, California; Department of Pediatric Dentistry, School of Dentistry, University of North Carolina, Chapel Hill, North Carolina; Herman Ostrow School of Dentistry, Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, California
| | - Michael L Paine
- Department of Basic Science and Craniofacial Biology, College of Dentistry, New York University, New York, New York; Department of Preventive and Restorative Dental Sciences, University of California, San Francisco, San Francisco, California; Department of Pediatric Dentistry, School of Dentistry, University of North Carolina, Chapel Hill, North Carolina; Herman Ostrow School of Dentistry, Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, California
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Hu Y, Smith CE, Cai Z, Donnelly LAJ, Yang J, Hu JCC, Simmer JP. Enamel ribbons, surface nodules, and octacalcium phosphate in C57BL/6 Amelx-/- mice and Amelx+/- lyonization. Mol Genet Genomic Med 2016; 4:641-661. [PMID: 27896287 PMCID: PMC5118209 DOI: 10.1002/mgg3.252] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/07/2016] [Accepted: 09/13/2016] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Amelogenin is required for normal enamel formation and is the most abundant protein in developing enamel. METHODS Amelx+/+, Amelx+/- , and Amelx-/- molars and incisors from C57BL/6 mice were characterized using RT-PCR, Western blotting, dissecting and light microscopy, immunohistochemistry (IHC), transmission electron microscopy (TEM), scanning electron microscopy (SEM), backscattered SEM (bSEM), nanohardness testing, and X-ray diffraction. RESULTS No amelogenin protein was detected by Western blot analyses of enamel extracts from Amelx-/- mice. Amelx-/- incisor enamel averaged 20.3 ± 3.3 μm in thickness, or only 1/6th that of the wild type (122.3 ± 7.9 μm). Amelx-/- incisor enamel nanohardness was 1.6 Gpa, less than half that of wild-type enamel (3.6 Gpa). Amelx+/- incisors and molars showed vertical banding patterns unique to each tooth. IHC detected no amelogenin in Amelx-/- enamel and varied levels of amelogenin in Amelx+/- incisors, which correlated positively with enamel thickness, strongly supporting lyonization as the cause of the variations in enamel thickness. TEM analyses showed characteristic mineral ribbons in Amelx+/+ and Amelx-/- enamel extending from mineralized dentin collagen to the ameloblast. The Amelx-/- enamel ribbons were not well separated by matrix and appeared to fuse together, forming plates. X-ray diffraction determined that the predominant mineral in Amelx-/- enamel is octacalcium phosphate (not calcium hydroxyapatite). Amelx-/- ameloblasts were similar to wild-type ameloblasts except no Tomes' processes extended into the thin enamel. Amelx-/- and Amelx+/- molars both showed calcified nodules on their occlusal surfaces. Histology of D5 and D11 developing molars showed nodules forming during the maturation stage. CONCLUSION Amelogenin forms a resorbable matrix that separates and supports, but does not shape early secretory-stage enamel ribbons. Amelogenin may facilitate the conversion of enamel ribbons into hydroxyapatite by inhibiting the formation of octacalcium phosphate. Amelogenin is necessary for thickening the enamel layer, which helps maintain ribbon organization and development and maintenance of the Tomes' process.
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Affiliation(s)
- Yuanyuan Hu
- Department of Biologic and Materials Sciences University of Michigan School of Dentistry 1210 Eisenhower Place Ann Arbor Michigan 48108
| | - Charles E Smith
- Department of Biologic and Materials SciencesUniversity of Michigan School of Dentistry1210Eisenhower PlaceAnn ArborMichigan48108; Facility for Electron Microscopy ResearchDepartment of Anatomy and Cell BiologyFaculty of DentistryMcGill UniversityMontrealQuebecH3A 2B2Canada
| | - Zhonghou Cai
- Advanced Photon Source Argonne National Laboratory 9700 S. Cass Ave Building 431-B005 Argonne Illinois 60439
| | - Lorenza A-J Donnelly
- Department of Biologic and Materials Sciences University of Michigan School of Dentistry 1210 Eisenhower Place Ann Arbor Michigan 48108
| | - Jie Yang
- Department of Biologic and Materials SciencesUniversity of Michigan School of Dentistry1210Eisenhower PlaceAnn ArborMichigan48108; Department of Pediatric DentistrySchool and Hospital of StomatologyPeking University22 South AvenueZhongguancun Haidian DistrictBeijing100081China
| | - Jan C-C Hu
- Department of Biologic and Materials Sciences University of Michigan School of Dentistry 1210 Eisenhower Place Ann Arbor Michigan 48108
| | - James P Simmer
- Department of Biologic and Materials Sciences University of Michigan School of Dentistry 1210 Eisenhower Place Ann Arbor Michigan 48108
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Evolutionary analysis of selective constraints identifies ameloblastin (AMBN) as a potential candidate for amelogenesis imperfecta. BMC Evol Biol 2015. [PMID: 26223266 PMCID: PMC4518657 DOI: 10.1186/s12862-015-0431-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
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.
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Gasse B, Grabar S, Lafont AG, Quinquis L, Opsahl Vital S, Davit-Béal T, Moulis E, Chabadel O, Hennequin M, Courson F, Droz D, Vaysse F, Laboux O, Tassery H, Al-Hashimi N, Boillot A, Carel JC, Treluyer JM, Jeanpierre M, Beldjord C, Sire JY, Chaussain C. Common SNPs of AmelogeninX (AMELX) and dental caries susceptibility. J Dent Res 2013; 92:418-24. [PMID: 23525533 DOI: 10.1177/0022034513482941] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Genetic approaches have shown that several genes could modify caries susceptibility; AmelogeninX (AMELX) has been repeatedly designated. Here, we hypothesized that AMELX mutations resulting in discrete changes of enamel microstructure may be found in children with a severe caries phenotype. In parallel, possible AMELX mutations that could explain resistance to caries may be found in caries-free patients. In this study, coding exons of AMELX and exon-intron boundaries were sequenced in 399 individuals with extensive caries (250) or caries-free (149) individuals from nine French hospital groups. No mutation responsible for a direct change of amelogenin function was identified. Seven single-nucleotide polymorphisms (SNPs) were found, 3 presenting a high allele frequency, and 1 being detected for the first time. Three SNPs were located in coding regions, 2 of them being non-synonymous. Both evolutionary and statistical analyses showed that none of these SNPs was associated with caries susceptibility, suggesting that AMELX is not a gene candidate in our studied population.
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Affiliation(s)
- B Gasse
- UMR 7138, Université Pierre et Marie Curie, 75005 Paris, France
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Zhang X, Diekwisch TGH, Luan X. Structure and function of ameloblastin as an extracellular matrix protein: adhesion, calcium binding, and CD63 interaction in human and mouse. Eur J Oral Sci 2012; 119 Suppl 1:270-9. [PMID: 22243256 DOI: 10.1111/j.1600-0722.2011.00889.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The functional significance of extracellular matrix proteins in the life of vertebrates is underscored by a high level of sequence variability in tandem with a substantial degree of conservation in terms of cell-cell and cell-matrix adhesion interactions. Many extracellular matrix proteins feature multiple adhesion domains for successful attachment to substrates, such as integrin, CD63, and heparin. Here we have used homology and ab initio modeling algorithms to compare mouse ameloblastin (mAMBN) and human ameloblastin (hABMN) isoforms and to analyze their potential for cell adhesion and interaction with other matrix molecules as well as calcium binding. Sequence comparison between mAMBN and hAMBN revealed a 26-amino-acid deletion in mAMBN, corresponding to a helix-loop-helix frameshift. The human AMBN domain (174Q-201G), homologous to the mAMBN 157E-178I helix-loop-helix region, formed a helix-loop motif with an extended loop, suggesting a higher degree of flexibility of hAMBN compared with mAMBN, as confirmed by molecular dynamics simulation. Heparin-binding domains, CD63-interaction domains, and calcium-binding sites in both hAMBN and mAMBN support the concept of AMBN as an extracellular matrix protein. The high level of conservation between AMBN functional domains related to adhesion and differentiation was remarkable when compared with only 61% amino acid sequence homology.
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Affiliation(s)
- Xu Zhang
- Brodie Laboratory for Craniofacial Genetics, University of Illinois - Chicago, Chicago, IL 60612, USA
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Al-Hashimi N, Sire JY, Delgado S. Evolutionary analysis of mammalian enamelin, the largest enamel protein, supports a crucial role for the 32-kDa peptide and reveals selective adaptation in rodents and primates. J Mol Evol 2010; 69:635-56. [PMID: 20012271 DOI: 10.1007/s00239-009-9302-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 11/06/2009] [Indexed: 12/20/2022]
Abstract
Enamelin (ENAM) plays an important role in the mineralization of the forming enamel matrix. We have performed an evolutionary analysis of mammalian ENAM to identify highly conserved residues or regions that could have important function (selective pressure), to predict mutations that could be associated with amelogenesis imperfecta in humans, and to identify possible adaptive evolution of ENAM during 200 million years ago of mammalian evolution. In order to fulfil these objectives, we obtained 36-ENAM sequences that are representative of the mammalian lineages. Our results show a remarkably high conservation pattern in the region of the 32-kDa fragment of ENAM, especially its phosphorylation, glycosylation, and proteolytic sites. In primates and rodents we also identified several sites under positive selection, which could indicate recent evolutionary changes in ENAM function. Furthermore, the analysis of the unusual signal peptide provided new insights on the possible regulation of ENAM secretion, a hypothesis that should be tested in the near future. Taken together, these findings improve our understanding of ENAM evolution and provide new information that would be useful for further investigation of ENAM function as well as for the validation of mutations leading to amelogenesis imperfecta.
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Affiliation(s)
- Nawfal Al-Hashimi
- Université Pierre et Marie Curie, UMR 7138-Systématique, Adaptation, Evolution, Case 5, 7 Quai Saint-Bernard, Bâtiment A, 4e étage, 75005, Paris, France
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Bardet C, Delgado S, Sire JY. MEPE evolution in mammals reveals regions and residues of prime functional importance. Cell Mol Life Sci 2010; 67:305-20. [PMID: 19924383 PMCID: PMC11115541 DOI: 10.1007/s00018-009-0185-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Revised: 10/13/2009] [Accepted: 10/14/2009] [Indexed: 01/17/2023]
Abstract
In mammals, the matrix extracellular phosphoglycoprotein (MEPE) is known to activate osteogenesis and mineralization via a particular region called dentonin, and to inhibit mineralization via its ASARM (acidic serine-aspartate rich MEPE-associated motif) peptide that also plays a role in phosphatemia regulation. In order to understand MEPE evolution in mammals, and particularly that of its functional regions, we conducted an evolutionary analysis based on the study of selective pressures. Using 37 mammalian sequences we: (1) confirmed the presence of an additional coding exon in most placentals; (2) highlighted several conserved residues and regions that could have important functions; (3) found that dentonin function was recruited in a placental ancestor; and (4) revealed that ASARM function was present earlier, pushing the recruitment of MEPE deep into amniote origins. Our data indicate that MEPE was involved in various functions (bone and eggshell mineralization) prior to acquiring those currently known in placental mammals.
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Affiliation(s)
- Claire Bardet
- UMR 7138, Equipe “Evolution & Développement du Squelette” Université Paris 6, Paris, France
| | - Sidney Delgado
- UMR 7138, Equipe “Evolution & Développement du Squelette” Université Paris 6, Paris, France
| | - Jean-Yves Sire
- UMR 7138, Equipe “Evolution & Développement du Squelette” Université Paris 6, Paris, France
- UMR 7138, Université Pierre et Marie Curie-Paris 6, Case 05, 7 Quai St-Bernard, 75005 Paris, France
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14
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Witten PE, Huysseune A. A comparative view on mechanisms and functions of skeletal remodelling in teleost fish, with special emphasis on osteoclasts and their function. Biol Rev Camb Philos Soc 2009; 84:315-46. [PMID: 19382934 DOI: 10.1111/j.1469-185x.2009.00077.x] [Citation(s) in RCA: 211] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Resorption and remodelling of skeletal tissues is required for development and growth, mechanical adaptation, repair, and mineral homeostasis of the vertebrate skeleton. Here we review for the first time the current knowledge about resorption and remodelling of the skeleton in teleost fish, the largest and most diverse group of extant vertebrates. Teleost species are increasingly used in aquaculture and as models in biomedical skeletal research. Thus, detailed knowledge is required to establish the differences and similarities between mammalian and teleost skeletal remodelling, and between distantly related species such as zebrafish (Danio rerio) and medaka (Oryzias latipes). The cellular mechanisms of differentiation and activation of osteoclasts and the functions of teleost skeletal remodelling are described. Several characteristics, related to skeletal remodelling, distinguish teleosts from mammals. These characteristics include (a) the absence of osteocytes in most species; (b) the absence of haematopoietic bone marrow tissue; (c) the abundance of small mononucleated osteoclasts performing non-lacunar (smooth) bone resorption, in addition to or instead of multinucleated osteoclasts; and (d) a phosphorus- rather than calcium-driven mineral homeostasis (mainly affecting the postcranial dermal skeleton). Furthermore, (e) skeletal resorption is often absent from particular sites, due to sparse or lacking endochondral ossification. Based on the mode of skeletal remodelling in early ontogeny of all teleosts and in later stages of development of teleosts with acellular bone we suggest a link between acellular bone and the predominance of mononucleated osteoclasts, on the one hand, and cellular bone and multinucleated osteoclasts on the other. The evolutionary origin of skeletal remodelling is discussed and whether mononucleated osteoclasts represent an ancestral type of resorbing cells. Revealing the differentiation and activation of teleost skeletal resorbing cells, in the absence of several factors that trigger mammalian osteoclast differentiation, is a current challenge. Understanding which characters of teleost bone remodelling are derived and which characters are conserved should enhance our understanding of the process in fish and may provide insights into alternative pathways of bone remodelling in mammals.
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15
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Cai J, Cho SW, Ishiyama M, Mikami M, Hosoya A, Kozawa Y, Ohshima H, Jung HS. Chick tooth induction revisited. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2009; 312B:465-72. [PMID: 19226602 DOI: 10.1002/jez.b.21265] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Teeth have been missing from Aves for almost 100 million years. However, it is believed that the avian oral epithelium retains the molecular signaling required to induce odontogenesis, and this has been widely examined using heterospecific recombinations with mouse dental mesenchyme. It has also been argued that teeth can form from the avian oral epithelium owing to contamination of the mouse mesenchyme with mouse dental epithelial cells. To investigate the possibility of tooth formation from chick oral epithelium and the characteristics of possible chick enamel, we applied LacZ transgenic mice during heterospecific recombination and examined the further tooth formation. Transmission electron microscopy was used to identify the two tissues during development after heterospecific recombination. No mixing was detected between chick oral epithelium and mouse dental mesenchyme after 2 days, and secretory ameloblasts with Tomes' processes were observed after 1 week. Teeth were formed after 3 weeks with a single cusp pattern, possibly determined by epithelial factors, which is similar to that of the avian tooth in the late Jurassic period. These recombinant teeth were smaller than mouse molars, whereas perfect structures of both ameloblasts and enamel showed histological characteristics similar to those of mice. Together these observations consistent with previous report that odontogenesis is initially directed by species-specific mesenchymal signals interplaying with common epithelial signals.
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Affiliation(s)
- Jinglei Cai
- Division in Anatomy and Developmental Biology, Department of Oral Biology, Research Center for Orofacial Hard Tissue Regeneration, College of Dentistry, Yonsei Center of Biotechnology, Yonsei University, Seoul, Korea
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16
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Morrill BH, Rickords LF, Schafstall HJ. Sequence length polymorphisms within primate amelogenin and amelogenin-like genes: usefulness in sex determination. Am J Primatol 2008; 70:976-85. [PMID: 18613027 DOI: 10.1002/ajp.20590] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Sequence length polymorphisms between the amelogenin (AMELX) and the amelogenin-like (AMELY) genes both within and between several mammalian species have been identified and utilized for sex determination, species identification, and to elucidate evolutionary relationships. Sex determination via polymerase chain reaction (PCR) assays of the AMELX and AMELY genes has been successful in greater apes, prosimians, and two species of old world monkeys. To date, no sex determination PCR assay using AMELX and AMELY has been developed for new world monkeys. In this study, we present partial AMELX and AMELY sequences for five old world monkey species (Mandrillus sphinx, Macaca nemestrina, Macaca fuscata, Macaca mulatta, and Macaca fascicularis) along with primer sets that can be used for sex determination of these five species. In addition, we compare the sequences we generated with other primate AMELX and AMELY sequences available on GenBank and discuss sequence length polymorphisms and their usefulness in sex determination within primates. The mandrill and four species of macaque all share two similar deletion regions with each other, the human, and the chimpanzee in the region sequenced. These two deletion regions are 176-181 and 8 nucleotides in length. In analyzing existing primate sequences on GenBank, we also discovered that a separate six-nucleotide polymorphism located approximately 300 nucleotides upstream of the 177 nucleotide polymorphism in sequences of humans and chimps was also present in two species of new world monkeys (Saimiri boliviensis and Saimiri sciureus). We designed primers that incorporate this polymorphism, creating the first AMELX and AMELY PCR primer set that has been used successfully to generate two bands in a new world monkey species.
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Affiliation(s)
- Benson H Morrill
- Department of Animal, Dairy, and Veterinary Science, Utah State University, Logan, Utah 84322-4815, USA
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17
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Bosshardt DD. Biological mediators and periodontal regeneration: a review of enamel matrix proteins at the cellular and molecular levels. J Clin Periodontol 2008; 35:87-105. [DOI: 10.1111/j.1600-051x.2008.01264.x] [Citation(s) in RCA: 194] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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18
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Richard B, Delgado S, Gorry P, Sire JY. A study of polymorphism in human AMELX. Arch Oral Biol 2007; 52:1026-31. [PMID: 17645864 DOI: 10.1016/j.archoralbio.2007.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2007] [Revised: 05/30/2007] [Accepted: 06/14/2007] [Indexed: 11/21/2022]
Abstract
Amelogenin gene (AMEL) encodes for a protein that plays important roles in the organization and structure of enamel. A recent evolutionary analysis of AMELX in mammals has revealed, aside to well-conserved 5' and 3' regions, a variable region located in the largest exon (exon 6), which strongly suggested the possible existence of polymorphism in human AMELX. A detailed analysis of this region was of fundamental importance for genetic studies. We have looked for variations in human AMELX exon 6 from 100 AMELX alleles in a randomized European population, using denaturing high-performance liquid chromatography (dHPLC). We also have looked for AMELX variants in databases, and compared this region in nine primates. There were no variations in the AMELX sequences analysed, but two synonymous single-nucleotide polymorphisms were found in databases. Alignment of the primate exon 6 sequences revealed that AMELX is highly constrained, as illustrated by 100% nucleotide identity found between humans and chimpanzee, and from 99.9 to 94.8% nucleotide identity in the other species. In contrast to what was suspected from the evolutionary analysis, we conclude that AMELX polymorphism should occur at low level in humans. This finding leads us to speculate that the high constraint observed in primate AMELX is related to its location on the X chromosome, and is due to selection at a single locus.
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19
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Kawasaki K, Buchanan AV, Weiss KM. Gene Duplication and the Evolution of Vertebrate Skeletal Mineralization. Cells Tissues Organs 2007; 186:7-24. [PMID: 17627116 DOI: 10.1159/000102678] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
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.
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Affiliation(s)
- Kazuhiko Kawasaki
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA.
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20
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Sire JY, Davit-Béal T, Delgado S, Gu X. The Origin and Evolution of Enamel Mineralization Genes. Cells Tissues Organs 2007; 186:25-48. [PMID: 17627117 DOI: 10.1159/000102679] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
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.
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Affiliation(s)
- Jean-Yves Sire
- UMR 7138, Université Pierre et Marie Curie-Paris 6, Paris, France.
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21
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Spahr A, Lyngstadaas SP, Slaby I, Pezeshki G. Ameloblastin expression during craniofacial bone formation in rats. Eur J Oral Sci 2007; 114:504-11. [PMID: 17184233 DOI: 10.1111/j.1600-0722.2006.00403.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Based on previous results showing the expression of ameloblastin (Ambn; amelin) in the formation of mesenchymal dental hard tissues, we investigated its presence during bone development. Immunohistochemistry (IHC), in situ hybridization (ISH), and reverse transcription-polymerase chain reaction (RT-PCR) were used to investigate the expression of ameloblastin protein and mRNA during craniofacial development in rats. Tissue samples were collected on embryonic day 18 and from days 2-28 postnatally. IHC revealed the expression of ameloblastin during bone formation at embryonic and early postnatal stages with different patterns of expression in intramembranous and endochondral ossification. In intramembranous ossification, ameloblastin expression was detected in the superficial layer of the condensed vascularized primitive connective tissue and in the cellular layer covering the surface of the newly formed woven bone. In endochondral ossification, ameloblastin was expressed within the extracellular matrix of the cartilage templates and in the perichondrium. Between days 2 and 28 the expression decreased markedly, concordant with the maturation of the bone, and disappeared after completion of bone remodeling. The results obtained by IHC were confirmed by ISH and RT-PCR, showing the expression of ameloblastin mRNA during craniofacial bone formation. This study indicates the expression of the putative dental protein ameloblastin during craniofacial bone development in rats.
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Affiliation(s)
- Axel Spahr
- Department Of Conservative Dentistry and Periodontology, University of Ulm, Ulm, Germany.
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22
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Davit-Béal T, Allizard F, Sire JY. Enameloid/enamel transition through successive tooth replacements in Pleurodeles waltl (Lissamphibia, Caudata). Cell Tissue Res 2006; 328:167-83. [PMID: 17180599 DOI: 10.1007/s00441-006-0306-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2006] [Accepted: 07/13/2006] [Indexed: 10/23/2022]
Abstract
Study of the evolutionary enameloid/enamel transition suffers from discontinuous data in the fossil record, although a developmental enameloid/enamel transition exists in living caudates, salamanders and newts. The timing and manner in which the enameloid/enamel transition is achieved during caudate ontogeny is of great interest, because the caudate situation could reflect events that have occurred during evolution. Using light and transmission electron microscopy, we have monitored the formation of the upper tooth region in six successive teeth of a tooth family (position I) in Pleurodeles waltl from late embryos to young adult. Enameloid has only been identified in embryonic tooth I(1) and in larval teeth I(2) and I(3). A thin layer of enamel is deposited later by ameloblasts on the enameloid surface of these teeth. From post-metamorphic juvenile onwards, teeth are covered with enamel only. The collagen-rich enameloid matrix is deposited by odontoblasts, which subsequently form dentin. Enameloid, like enamel, mineralizes and then matures but ameloblast participation in enameloid matrix deposition has not been established. From tooth I(1) to tooth I(3), the enameloid matrix becomes ever more dense and increasingly comes to resemble the dentin matrix, although it is still subjected to maturation. Our data suggest the absence of an enameloid/enamel transition and, instead, the occurrence of an enameloid/dentin transition, which seems to result from a progressive slowing down of odontoblast activity. As a consequence, the ameloblasts in post-metamorphic teeth appear to synthesize the enamel matrix earlier than in larval teeth.
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Affiliation(s)
- T Davit-Béal
- Equipe Evolution and Développement du Squelette, UMR 7138, Systématique, Adaptations, Evolution, UPMC-CNRS-MNHN-IRD, Université Paris 6, Paris Cedex 05, France
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