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Delgado S, Fernandez-Trujillo MA, Houée G, Silvent J, Liu X, Corre E, Sire JY. Expression of 20 SCPP genes during tooth and bone mineralization in Senegal bichir. Dev Genes Evol 2023; 233:91-106. [PMID: 37410100 DOI: 10.1007/s00427-023-00706-w] [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: 01/12/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023]
Abstract
The African bichir (Polypterus senegalus) is a living representative of Polypteriformes. P. senegalus possesses teeth composed of dentin covered by an enameloid cap and a layer of collar enamel on the tooth shaft, as in lepisosteids. A thin layer of enamel matrix can also be found covering the cap enameloid after its maturation and during the collar enamel formation. Teleosts fish do not possess enamel; teeth are protected by cap and collar enameloid, and inversely in sarcopterygians, where teeth are only covered by enamel, with the exception of the cap enameloid in teeth of larval urodeles. The presence of enameloid and enamel in the teeth of the same organism is an opportunity to solve the evolutionary history of the presence of enamel/enameloid in basal actinopterygians. In silico analyses of the jaw transcriptome of a juvenile bichir provided twenty SCPP transcripts. They included enamel, dentin, and bone-specific SCPPs known in sarcopterygians and several actinopterygian-specific SCPPs. The expression of these 20 genes was investigated by in situ hybridizations on jaw sections during tooth and dentary bone formation. A spatiotemporal expression patterns were established and compared with previous studies of SCPP gene expression during enamel/enameloid and bone formation. Similarities and differences were highlighted, and several SCPP transcripts were found specifically expressed during tooth or bone formation suggesting either conserved or new functions of these SCPPs.
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Affiliation(s)
- S Delgado
- Sorbonne Université, MNHN, CNRS, EPHE, Institut Systématique Évolution Biodiversité, ISYEB, Equipe Homologies, 75005, Paris, France.
| | - M A Fernandez-Trujillo
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7138, Equipe Evolution et Développement du Squelette, 75005, Paris, France
| | - G Houée
- Sorbonne Université, Muséum National d'Histoire Naturelle, CNRS, CR2P (Centre de Recherche en Paléontologie - Paris), UMR 7207, Equipe Formes, Structures et Fonctions, 43 rue Buffon, 75005, Paris, France
| | - J Silvent
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7138, Equipe Evolution et Développement du Squelette, 75005, Paris, France
| | - X Liu
- Sorbonne Université - CNRS, FR2424, Station Biologique de Roscoff, Plateforme ABiMS (Analysis and Bioinformatics for Marine Science), 29680, Roscoff, France
| | - E Corre
- Sorbonne Université - CNRS, FR2424, Station Biologique de Roscoff, Plateforme ABiMS (Analysis and Bioinformatics for Marine Science), 29680, Roscoff, France
| | - J Y Sire
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7138, Equipe Evolution et Développement du Squelette, 75005, Paris, France
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Kawasaki K, Sasagawa I, Mikami M, Nakatomi M, Ishiyama M. Ganoin and acrodin formation on scales and teeth in spotted gar: A vital role of enamelin in the unique process of enamel mineralization. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:455-468. [PMID: 36464775 PMCID: PMC10239528 DOI: 10.1002/jez.b.23183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/12/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022]
Abstract
Gars and bichirs develop scales and teeth with ancient actinopterygian characteristics. Their scale surface and tooth collar are covered with enamel, also known as ganoin, whereas the tooth cap is equipped with an enamel-like tissue, acrodin. Here, we investigated the formation and mineralization of the ganoin and acrodin matrices in spotted gar, and the evolution of the scpp5, ameloblastin (ambn), and enamelin (enam) genes, which encode matrix proteins of ganoin. Results suggest that, in bichirs and gars, all these genes retain structural characteristics of their orthologs in stem actinopterygians, presumably reflecting the presence of ganoin on scales and teeth. During scale formation, Scpp5 and Enam were initially found in the incipient ganoin matrix and the underlying collagen matrix, whereas Ambn was detected mostly in a surface region of the well-developed ganoin matrix. Although collagen is the principal acrodin matrix protein, Scpp5 was detected within the matrix. Similarities in timings of mineralization and the secretion of Scpp5 suggest that acrodin evolved by the loss of the matrix secretory stage of ganoin formation: dentin formation is immediately followed by the maturation stage. The late onset of Ambn secretion during ganoin formation implies that Ambn is not essential for mineral ribbon formation, the hallmark of the enamel matrix. Furthermore, Scpp5 resembles amelogenin that is not important for the initial formation of mineral ribbons in mammals. It is thus likely that the evolution of ENAM was vital to the origin of the unique mineralization process of the enamel matrix.
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Affiliation(s)
- Kazuhiko Kawasaki
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Ichiro Sasagawa
- Advanced Research Center, School of Life Dentistry at Niigata the Nippon Dental University, Niigata, Japan
| | - Masato Mikami
- Department of Microbiology, School of Life Dentistry at Niigata the Nippon Dental University, Niigata, Japan
| | - Mitsushiro Nakatomi
- Department of Human, Information and Life Sciences, School of Health Sciences, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Mikio Ishiyama
- Department of Histology, School of Life Dentistry at Niigata the Nippon Dental University, Niigata, Japan
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Petersen AM, Small CM, Yan Y, Wilson C, Batzel P, Bremiller RA, Buck CL, von Hippel FA, Cresko WA, Postlethwait JH. Evolution and developmental expression of the sodium-iodide symporter ( NIS, slc5a5) gene family: Implications for perchlorate toxicology. Evol Appl 2022; 15:1079-1098. [PMID: 35899258 PMCID: PMC9309457 DOI: 10.1111/eva.13424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 11/27/2022] Open
Abstract
The vertebrate sodium-iodide symporter (NIS or SLC5A5) transports iodide into the thyroid follicular cells that synthesize thyroid hormone. The SLC5A protein family includes transporters of vitamins, minerals, and nutrients. Disruption of SLC5A5 function by perchlorate, a pervasive environmental contaminant, leads to human pathologies, especially hypothyroidism. Perchlorate also disrupts the sexual development of model animals, including threespine stickleback (Gasterosteus aculeatus) and zebrafish (Danio rerio), but the mechanism of action is unknown. To test the hypothesis that SLC5A5 paralogs are expressed in tissues necessary for the development of reproductive organs, and therefore are plausible candidates to mediate the effects of perchlorate on sexual development, we first investigated the evolutionary history of Slc5a paralogs to better understand potential functional trajectories of the gene family. We identified two clades of slc5a paralogs with respect to an outgroup of sodium/choline cotransporters (slc5a7); these clades are the NIS clade of sodium/iodide and lactate cotransporters (slc5a5, slc5a6, slc5a8, slc5a8, and slc5a12) and the SGLT clade of sodium/glucose cotransporters (slc5a1, slc5a2, slc5a3, slc5a4, slc5a10, and slc5a11). We also characterized expression patterns of slc5a genes during development. Stickleback embryos and early larvae expressed NIS clade genes in connective tissue, cartilage, teeth, and thyroid. Stickleback males and females expressed slc5a5 and its paralogs in gonads. Single-cell transcriptomics (scRNA-seq) on zebrafish sex-genotyped gonads revealed that NIS clade-expressing cells included germ cells (slc5a5, slc5a6a, and slc5a6b) and gonadal soma cells (slc5a8l). These results are consistent with the hypothesis that perchlorate exerts its effects on sexual development by interacting with slc5a5 or its paralogs in reproductive tissues. These findings show novel expression domains of slc5 genes in stickleback and zebrafish, which suggest similar functions across vertebrates including humans, and provide candidates to mediate the effects of perchlorate on sexual development.
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Affiliation(s)
- Ann M. Petersen
- Department of Biology, Institute of Ecology and EvolutionUniversity of OregonEugeneOregonUSA
- J.J. Howard Marine Lab, Northeast Fisheries Science CenterNational Oceanographic and Atmospheric AdministrationSandy HookNew JerseyUSA
| | - Clayton M. Small
- Department of Biology, Institute of Ecology and EvolutionUniversity of OregonEugeneOregonUSA
| | - Yi‐Lin Yan
- Department of Biology, Institute of NeuroscienceUniversity of OregonEugeneOregonUSA
| | - Catherine Wilson
- Department of Biology, Institute of NeuroscienceUniversity of OregonEugeneOregonUSA
| | - Peter Batzel
- Department of Biology, Institute of NeuroscienceUniversity of OregonEugeneOregonUSA
| | - Ruth A. Bremiller
- Department of Biology, Institute of NeuroscienceUniversity of OregonEugeneOregonUSA
| | - C. Loren Buck
- Department of Biological SciencesNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Frank A. von Hippel
- Department of Community, Environment & Policy, Mel & Enid Zuckerman College of Public HealthUniversity of ArizonaTucsonArizonaUSA
| | - William A. Cresko
- Department of Biology, Institute of Ecology and EvolutionUniversity of OregonEugeneOregonUSA
| | - John H. Postlethwait
- Department of Biology, Institute of NeuroscienceUniversity of OregonEugeneOregonUSA
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Leurs N, Martinand-Mari C, Marcellini S, Debiais-Thibaud M. Parallel evolution of ameloblastic scpp genes in bony and cartilaginous vertebrates. Mol Biol Evol 2022; 39:6582990. [PMID: 35535508 PMCID: PMC9122587 DOI: 10.1093/molbev/msac099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
In bony vertebrates, skeletal mineralization relies on the secretory calcium-binding phosphoproteins (Scpp) family whose members are acidic extracellular proteins posttranslationally regulated by the Fam20°C kinase. As scpp genes are absent from the elephant shark genome, they are currently thought to be specific to bony fishes (osteichthyans). Here, we report a scpp gene present in elasmobranchs (sharks and rays) that evolved from local tandem duplication of sparc-L 5′ exons and show that both genes experienced recent gene conversion in sharks. The elasmobranch scpp is remarkably similar to the osteichthyan scpp members as they share syntenic and gene structure features, code for a conserved signal peptide, tyrosine-rich and aspartate/glutamate-rich regions, and harbor putative Fam20°C phosphorylation sites. In addition, the catshark scpp is coexpressed with sparc-L and fam20°C in tooth and scale ameloblasts, similarly to some osteichthyan scpp genes. Despite these strong similarities, molecular clock and phylogenetic data demonstrate that the elasmobranch scpp gene originated independently from the osteichthyan scpp gene family. Our study reveals convergent events at the sparc-L locus in the two sister clades of jawed vertebrates, leading to parallel diversification of the skeletal biomineralization toolkit. The molecular evolution of sparc-L and its coexpression with fam20°C in catshark ameloblasts provides a unifying genetic basis that suggests that all convergent scpp duplicates inherited similar features from their sparc-L precursor. This conclusion supports a single origin for the hypermineralized outer odontode layer as produced by an ancestral developmental process performed by Sparc-L, implying the homology of the enamel and enameloid tissues in all vertebrates.
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Affiliation(s)
- Nicolas Leurs
- Institut des Sciences de l'Evolution de Montpellier, ISEM, Univ Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Camille Martinand-Mari
- Institut des Sciences de l'Evolution de Montpellier, ISEM, Univ Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Sylvain Marcellini
- Departamento de Biología Celular, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
| | - Mélanie Debiais-Thibaud
- Institut des Sciences de l'Evolution de Montpellier, ISEM, Univ Montpellier, CNRS, IRD, EPHE, Montpellier, France
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Abstract
Scales, as key structures of fish skin, play an important role in physiological function. The study of fish scale development mechanisms provides a basis for exploring the molecular-level developmental differences between scaled and non-scaled fishes. In this study, alizarin red staining was used to divide the different stages of zebrafish (Danio rerio) scale development. Four developmental stages, namely stage I (~17 dpf, scales have not started to grow), stage II (~33 dpf, the point at which scales start to grow), stage III (~41 dpf, the period in which the scales almost cover the whole body), and stage IV (~3 mpf, scales cover the whole body), were determined and used for subsequent transcriptome analysis. WGCNA (weighted correlation network analysis) and DEG (differentially expressed gene) analysis were used for screening the key genes. Based on the comparison between stage II and stage I, 54 hub-genes were identified by WGCNA analysis. Key genes including the Scpp family (Scpp7, Scpp6, Scpp5, and Scpp8), the Fgf family (Fgfr1b and Fgfr3), Tcf7, Wnt10b, Runx2b, and Il2rb were identified by DEG analysis, which indicated that these genes played important roles in the key nodes of scale development signal pathways. Combined with this analysis, the TGF-β, Wnt/β-catenin, and FGF signaling pathways were suggested to be the most important signal pathways for scales starting to grow. This study laid a foundation for exploring the scale development mechanism of other fishes. The scale development candidate genes identified in the current study will facilitate functional gene identifications in the future.
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Convergent losses of SCPP genes and ganoid scales among non-teleost actinopterygians. Gene 2022; 811:146091. [PMID: 34864098 DOI: 10.1016/j.gene.2021.146091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/25/2021] [Accepted: 11/23/2021] [Indexed: 12/25/2022]
Abstract
Various secretory calcium-binding phosphoprotein (SCPP) genes are expressed in the skin and jaw during the formation of bone, teeth, and scales in osteichthyans (bony vertebrates). Among these mineralized skeletal units is the ganoid scale, found in many fossil actinopterygians (ray-finned fish) but confirmed only in Polypteriformes (bichirs, reedfish) and Lepisosteiformes (gars) among extant clades. Here, we examined SCPP genes in the genome of seven non-teleost actinopterygian species that possess or do not possess ganoid scales. As a result, 39-43 SCPP genes were identified in Polypteriformes and Lepisosteiformes, whereas 22-24 SCPP genes were found in Acipenseriformes (sturgeons, paddlefish) and Amiiformes (bowfin). Most of these genes form two clusters in the genome of Polypteriformes, Lepisosteiformes, and Amiiformes, and these two clusters are duplicated in Acipenseriformes. Despite their distant phylogenetic relationship, Polypteriformes and Lepisosteiformes retain many orthologous SCPP genes. These results imply that common ancestors of extant actinopterygians possessed a large repertoire of SCPP genes, and that many SCPP genes were lost independently in Acipenseriformes and Amiiformes. Notably, most SCPP genes originally located in one of the two SCPP gene clusters are retained in Polypteriformes and Lepisosteiformes but were secondarily lost in Acipenseriformes and Amiiformes. In Lepisosteiformes, orthologs of these lost genes show high or detectable expression levels in the skin but not in the jaw. We thus hypothesize that many SCPP genes located in this cluster are involved in the formation of ganoid scales in Polypteriformes and Lepisosteiformes, and that their orthologs and ganoid scales were convergently lost in Acipenseriformes and Amiiformes.
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Simmer JP, Hu JCC, Hu Y, Zhang S, Liang T, Wang SK, Kim JW, Yamakoshi Y, Chun YH, Bartlett JD, Smith CE. A genetic model for the secretory stage of dental enamel formation. J Struct Biol 2021; 213:107805. [PMID: 34715329 PMCID: PMC8665125 DOI: 10.1016/j.jsb.2021.107805] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 01/13/2023]
Abstract
The revolution in genetics has rapidly increased our knowledge of human and mouse genes that are critical for the formation of dental enamel and helps us understand how enamel evolved. In this graphical review we focus on the roles of 41 genes that are essential for the secretory stage of amelogenesis when characteristic enamel mineral ribbons initiate on dentin and elongate to expand the enamel layer to the future surface of the tooth. Based upon ultrastructural analyses of genetically modified mice, we propose a molecular model explaining how a cell attachment apparatus including collagen 17, α6ß4 and αvß6 integrins, laminin 332, and secreted enamel proteins could attach to individual enamel mineral ribbons and mold their cross-sectional dimensions as they simultaneously elongate and orient them in the direction of the retrograde movement of the ameloblast membrane.
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Affiliation(s)
- James P Simmer
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, 1011 North University, Ann Arbor, MI 48108, USA.
| | - Jan C-C Hu
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, 1011 North University, Ann Arbor, MI 48108, USA.
| | - Yuanyuan Hu
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, 1011 North University, Ann Arbor, MI 48108, USA.
| | - Shelly Zhang
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, 1011 North University, Ann Arbor, MI 48108, USA.
| | - Tian Liang
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, 1011 North University, Ann Arbor, MI 48108, USA.
| | - Shih-Kai Wang
- Department of Dentistry, National Taiwan University School of Dentistry, No. 1, Changde St., Zhongzheng Dist., Taipei City 100, Taiwan; Department of Pediatric Dentistry, National Taiwan University Children's Hospital, No. 8, Zhongshan S. Rd., Zhongzheng Dist., Taipei City 100, Taiwan.
| | - Jung-Wook Kim
- Department of Molecular Genetics, School of Dentistry & Dental Research Institute, Seoul National University, Seoul, Korea; Department of Pediatric Dentistry, School of Dentistry & Dental Research Institute, Seoul National University, Seoul, Korea.
| | - Yasuo Yamakoshi
- Department of Biochemistry and Molecular Biology, School of Dental Medicine, Tsurumi University, 2-1-3 Tsurumi, Tsurumi-ku, Yokohama 230-8501, Japan.
| | - Yong-Hee Chun
- Department of Periodontics, School of Dentistry, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
| | - John D Bartlett
- Division of Biosciences, Ohio State University College of Dentistry, Columbus, OH, USA.
| | - Charles E Smith
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, 1011 North University, Ann Arbor, MI 48108, USA; Department of Anatomy & Cell Biology, Faculty of Medicine & Health Sciences, McGill University, Montreal, Quebec H3A 0C7, Canada.
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Kawasaki K, Keating JN, Nakatomi M, Welten M, Mikami M, Sasagawa I, Puttick MN, Donoghue PC, Ishiyama M. Coevolution of enamel, ganoin, enameloid, and their matrix SCPP genes in osteichthyans. iScience 2021; 24:102023. [PMID: 33506188 PMCID: PMC7814152 DOI: 10.1016/j.isci.2020.102023] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/14/2020] [Accepted: 12/29/2020] [Indexed: 12/19/2022] Open
Abstract
We resolve debate over the evolution of vertebrate hypermineralized tissues through analyses of matrix protein-encoding secretory calcium-binding phosphoprotein (SCPP) genes and phylogenetic inference of hypermineralized tissues. Among these genes, AMBN and ENAM are found in both sarcopterygians and actinopterygians, whereas AMEL and SCPP5 are found only in sarcopterygians and actinopterygians, respectively. Actinopterygian AMBN, ENAM, and SCPP5 are expressed during the formation of hypermineralized tissues on scales and teeth: ganoin, acrodin, and collar enamel in gar, and acrodin and collar enameloid in zebrafish. Our phylogenetic analyses indicate the emergence of an ancestral enamel in stem-osteichthyans, whereas ganoin emerged in stem-actinopterygians and true enamel in stem-sarcopterygians. Thus, AMBN and ENAM originated in concert with ancestral enamel, SCPP5 evolved in association with ganoin, and AMEL evolved with true enamel. Shifts in gene expression domain and timing explain the evolution of different hypermineralized tissues. We propose that hypermineralized tissues in osteichthyans coevolved with matrix SCPP genes. Ganoin emerged in actinopterygians; true enamel arose in sarcopterygians Dental enamel, acrodin, and enameloid in actinopterygians are related to ganoin SCPP5 evolved in association with ganoin, whereas AMEL evolved with true enamel Shifts in SCPP gene expression explain the evolution of hypermineralized tissues
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Affiliation(s)
- Kazuhiko Kawasaki
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA
- Corresponding author
| | - Joseph N. Keating
- School of Earth Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - Mitsushiro Nakatomi
- Division of Anatomy, Kyushu Dental University, Kitakyushu, Fukuoka 803-8580, Japan
| | - Monique Welten
- School of Earth Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - Masato Mikami
- Department of Microbiology, School of Life Dentistry at Niigata, the Nippon Dental University, Niigata, Niigata 951-8580, Japan
| | - Ichiro Sasagawa
- Advanced Research Center, School of Life Dentistry at Niigata, the Nippon Dental University, Niigata, Niigata 951-8580, Japan
| | - Mark N. Puttick
- School of Earth Sciences, University of Bristol, Bristol BS8 1TQ, UK
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | | | - Mikio Ishiyama
- Department of Histology, School of Life Dentistry at Niigata, the Nippon Dental University, Niigata, Niigata 951-8580, Japan
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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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Zhang YH, Ravi V, Qin G, Dai H, Zhang HX, Han FM, Wang X, Liu YH, Yin JP, Huang LM, Venkatesh B, Lin Q. Comparative genomics reveal shared genomic changes in syngnathid fishes and signatures of genetic convergence with placental mammals. Natl Sci Rev 2020; 7:964-977. [PMID: 34692118 PMCID: PMC8289055 DOI: 10.1093/nsr/nwaa002] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 12/31/2019] [Accepted: 01/06/2020] [Indexed: 12/19/2022] Open
Abstract
Syngnathids (seahorses, pipefishes and seadragons) exhibit an array of morphological innovations including loss of pelvic fins, a toothless tubular mouth and male pregnancy. They comprise two subfamilies: Syngnathinae and Nerophinae. Genomes of three Syngnathinae members have been analyzed previously. In this study, we have sequenced the genome of a Nerophinae member, the Manado pipefish (Microphis manadensis), which has a semi-enclosed brood pouch. Comparative genomic analysis revealed that the molecular evolutionary rate of the four syngnathids is higher than that of other teleosts. The loss of all but one P/Q-rich SCPP gene in the syngnathids suggests a role for the lost genes in dentin and enameloid formation in teleosts. Genome-wide comparison identified a set of 118 genes with parallel identical amino acid substitutions in syngnathids and placental mammals. Association of some of these genes with placental and embryonic development in mammals suggests a role for them in syngnathid pregnancy.
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Affiliation(s)
- Yan-Hong Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Vydianathan Ravi
- Comparative and Medical Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR 138673, Singapore
| | - Geng Qin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - He Dai
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Hui-Xian Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Feng-Ming Han
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Xin Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Yu-Hong Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Jian-Ping Yin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Liang-Min Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Byrappa Venkatesh
- Comparative and Medical Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR 138673, Singapore
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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The Evolution of Unusually Small Amelogenin Genes in Cetaceans; Pseudogenization, X-Y Gene Conversion, and Feeding Strategy. J Mol Evol 2019; 88:122-135. [PMID: 31754761 DOI: 10.1007/s00239-019-09917-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 11/08/2019] [Indexed: 12/11/2022]
Abstract
Among extant cetaceans, mysticetes are filter feeders that do not possess teeth and use their baleen for feeding, while most odontocetes are considered suction feeders, which capture prey by suction without biting or chewing with teeth. In the present study, we address the functionality of amelogenin (AMEL) genes in cetaceans. AMEL encodes a protein that is specifically involved in dental enamel formation and is located on the sex chromosomes in eutherians. The X-copy AMELX is functional in enamel-bearing eutherians, whereas the Y-copy AMELY appears to have undergone decay and was completely lost in some species. Consistent with these premises, we detected various deleterious mutations and/or non-canonical splice junctions in AMELX of mysticetes and four suction feeding odontocetes, Delphinapterus leucas, Monodon monoceros, Kogia breviceps, and Physeter macrocephalus, and in AMELY of mysticetes and odontocetes. Regardless of the functionality, both AMELX and AMELY are equally and unusually small in cetaceans, and even their functional AMELX genes presumably encode a degenerate core region, which is thought to be essential for enamel matrix assembly and enamel crystal growth. Furthermore, our results suggest that the most recent common ancestors of extant cetaceans had functional AMELX and AMELY, both of which are similar to AMELX of Platanista minor. Similar small AMELX and AMELY in archaic cetaceans can be explained by gene conversion between AMELX and AMELY. We speculate that common ancestors of modern cetaceans employed a degenerate AMELX, transferred from a decaying AMELY by gene conversion, at an early stage of their transition to suction feeders.
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Zhang H, Hu Y, Seymen F, Koruyucu M, Kasimoglu Y, Wang S, Wright JT, Havel MW, Zhang C, Kim J, Simmer JP, Hu JC. ENAM mutations and digenic inheritance. Mol Genet Genomic Med 2019; 7:e00928. [PMID: 31478359 PMCID: PMC6785452 DOI: 10.1002/mgg3.928] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/25/2019] [Accepted: 07/26/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND ENAM mutations cause autosomal dominant or recessive amelogenesis imperfecta (AI) and show a dose effect: enamel malformations are more severe or only penetrant when both ENAM alleles are defective. METHODS Whole exome sequences of recruited AI probands were initially screened for mutations in known AI candidate genes. Sanger sequencing was used to confirm sequence variations and their segregation with the disease phenotype. The co-occurrence of ENAM and LAMA3 mutations in one family raised the possibility of digenic inheritance. Enamel formed in Enam+/+ Ambn+/+ , Enam+/- , Ambn+/- , and Enam+/- Ambn+/- mice was characterized by dissection and backscattered scanning electron microscopy (bSEM). RESULTS ENAM mutations segregating with AI in five families were identified. Two novel ENAM frameshift mutations were identified. A single-nucleotide duplication (c.395dupA/p.Pro133Alafs*13) replaced amino acids 133-1142 with a 12 amino acid (ATTKAAFEAAIT*) sequence, and a single-nucleotide deletion (c.2763delT/p.Asp921Glufs*32) replaced amino acids 921-1142 with 31 amino acids (ESSPQQASYQAKETAQRRGKAKTLLEMMCPR*). Three families were heterozygous for a previously reported single-nucleotide ENAM deletion (c.588+1delG/p.Asn197Ilefs*81). One of these families also harbored a heterozygous LAMA3 mutation (c.1559G>A/p.Cys520Tyr) that cosegregated with both the AI phenotype and the ENAM mutation. In mice, Ambn+/- maxillary incisors were normal. Ambn+/- molars were also normal, except for minor surface roughness. Ambn+/- mandibular incisors were sometimes chalky and showed minor chipping. Enam+/- incisor enamel was thinner than normal with ectopic mineral deposited laterally. Enam+/- molars were sometimes chalky and rough surfaced. Enam+/- Ambn+/- enamel was thin and rough, in part due to ectopic mineralization, but also underwent accelerated attrition. CONCLUSION Novel ENAM mutations causing AI were identified, raising to 22 the number of ENAM variations known to cause AI. The severity of the enamel phenotype in Enam+/- Ambn+/- double heterozygous mice is caused by composite digenic effects. Digenic inheritance should be explored as a cause of AI in humans.
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Affiliation(s)
- Hong Zhang
- Department of Biologic and Materials SciencesUniversity of Michigan School of DentistryAnn ArborMIUSA
| | - Yuanyuan Hu
- Department of Biologic and Materials SciencesUniversity of Michigan School of DentistryAnn ArborMIUSA
| | - Figen Seymen
- Department of Pedodontics, Faculty of DentistryIstanbul UniversityIstanbulTurkey
| | - Mine Koruyucu
- Department of Pedodontics, Faculty of DentistryIstanbul UniversityIstanbulTurkey
| | - Yelda Kasimoglu
- Department of Pedodontics, Faculty of DentistryIstanbul UniversityIstanbulTurkey
| | - Shih‐Kai Wang
- Department of Biologic and Materials SciencesUniversity of Michigan School of DentistryAnn ArborMIUSA
- Department of DentistryNational Taiwan University School of DentistryTaipei CityTaiwan R.O.C.
| | - John Timothy Wright
- Department of Pediatric DentistryUniversity of North Carolina School of DentistryChapel HillNCUSA
| | - Michael W. Havel
- Department of Biologic and Materials SciencesUniversity of Michigan School of DentistryAnn ArborMIUSA
| | - Chuhua Zhang
- Department of Biologic and Materials SciencesUniversity of Michigan School of DentistryAnn ArborMIUSA
| | - Jung‐Wook Kim
- Department of Molecular Genetics and Department of Pediatric Dentistry and Dental Research Institute, School of DentistrySeoul National UniversitySeoulKorea
| | - James P. Simmer
- Department of Biologic and Materials SciencesUniversity of Michigan School of DentistryAnn ArborMIUSA
| | - Jan C.‐C. Hu
- Department of Biologic and Materials SciencesUniversity of Michigan School of DentistryAnn ArborMIUSA
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13
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Liang T, Hu Y, Smith CE, Richardson AS, Zhang H, Yang J, Lin B, Wang S, Kim J, Chun Y, Simmer JP, Hu JC. AMBN mutations causing hypoplastic amelogenesis imperfecta and Ambn knockout-NLS-lacZ knockin mice exhibiting failed amelogenesis and Ambn tissue-specificity. Mol Genet Genomic Med 2019; 7:e929. [PMID: 31402633 PMCID: PMC6732285 DOI: 10.1002/mgg3.929] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/25/2019] [Accepted: 07/26/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Ameloblastin (AMBN) is a secreted matrix protein that is critical for the formation of dental enamel and is enamel-specific with respect to its essential functions. Biallelic AMBN defects cause non-syndromic autosomal recessive amelogenesis imperfecta. Homozygous Ambn mutant mice expressing an internally truncated AMBN protein deposit only a soft mineral crust on the surface of dentin. METHODS We characterized a family with hypoplastic amelogenesis imperfecta caused by AMBN compound heterozygous mutations (c.1061T>C; p.Leu354Pro/ c.1340C>T; p.Pro447Leu). We generated and characterized Ambn knockout/NLS-lacZ (AmbnlacZ/lacZ ) knockin mice. RESULTS No AMBN protein was detected using immunohistochemistry in null mice. ß-galactosidase activity was specific for ameloblasts in incisors and molars, and islands of cells along developing molar roots. AmbnlacZ/lacZ 7-week incisors and unerupted (D14) first molars showed extreme enamel surface roughness. No abnormalities were observed in dentin mineralization or in nondental tissues. Ameloblasts in the AmbnlacZ/lacZ mice were unable to initiate appositional growth and started to degenerate and deposit ectopic mineral. No layer of initial enamel ribbons formed in the AmbnlacZ/lacZ mice, but pockets of amelogenin accumulated on the dentin surface along the ameloblast distal membrane and within the enamel organ epithelia (EOE). NLS-lacZ signal was positive in the epididymis and nasal epithelium, but negative in ovary, oviduct, uterus, prostate, seminal vesicles, testis, submandibular salivary gland, kidney, liver, bladder, and bone, even after 15 hr of incubation with X-gal. CONCLUSIONS Ameloblastin is critical for the initiation of enamel ribbon formation, and its absence results in pathological mineralization within the enamel organ epithelia.
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Affiliation(s)
- Tian Liang
- Department of Biologic and Materials SciencesUniversity of Michigan School of DentistryAnn ArborMichigan
| | - Yuanyuan Hu
- Department of Biologic and Materials SciencesUniversity of Michigan School of DentistryAnn ArborMichigan
| | - Charles E. Smith
- Department of Anatomy and Cell Biology, Faculty of MedicineMcGill UniversityMontrealQuebecCanada
| | - Amelia S Richardson
- Department of Biologic and Materials SciencesUniversity of Michigan School of DentistryAnn ArborMichigan
| | - Hong Zhang
- Department of Biologic and Materials SciencesUniversity of Michigan School of DentistryAnn ArborMichigan
| | - Jie Yang
- Department of Biologic and Materials SciencesUniversity of Michigan School of DentistryAnn ArborMichigan
- Department of Pediatric Dentistry, School and Hospital of StomatologyPeking UniversityBeijingChina
| | - Brent Lin
- Department of Orofacial SciencesUCSF School of DentistrySan FranciscoCalifornia
| | - Shih‐Kai Wang
- Department of DentistryNational Taiwan University School of DentistryTaipei CityTaiwan R.O.C
| | - Jung‐Wook Kim
- Department of Molecular Genetics and Department of Pediatric Dentistry & Dental Research Institute, School of DentistrySeoul National UniversitySeoulKorea
| | - Yong‐Hee Chun
- Department of Periodontics and Department of Cell Systems & Anatomy, School of DentistryUniversity of Texas Health Science Center at San AntonioSan AntonioTexas
| | - James P. Simmer
- Department of Biologic and Materials SciencesUniversity of Michigan School of DentistryAnn ArborMichigan
| | - Jan C.‐C. Hu
- Department of Biologic and Materials SciencesUniversity of Michigan School of DentistryAnn ArborMichigan
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14
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Enault S, Muñoz D, Simion P, Ventéo S, Sire JY, Marcellini S, Debiais-Thibaud M. Evolution of dental tissue mineralization: an analysis of the jawed vertebrate SPARC and SPARC-L families. BMC Evol Biol 2018; 18:127. [PMID: 30165817 PMCID: PMC6117938 DOI: 10.1186/s12862-018-1241-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 08/15/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The molecular bases explaining the diversity of dental tissue mineralization across gnathostomes are still poorly understood. Odontodes, such as teeth and body denticles, are serial structures that develop through deployment of a gene regulatory network shared between all gnathostomes. Dentin, the inner odontode mineralized tissue, is produced by odontoblasts and appears well-conserved through evolution. In contrast, the odontode hypermineralized external layer (enamel or enameloid) produced by ameloblasts of epithelial origin, shows extensive structural variations. As EMP (Enamel Matrix Protein) genes are as yet only found in osteichthyans where they play a major role in the mineralization of teeth and others skeletal organs, our understanding of the molecular mechanisms leading to the mineralized odontode matrices in chondrichthyans remains virtually unknown. RESULTS We undertook a phylogenetic analysis of the SPARC/SPARC-L gene family, from which the EMPs are supposed to have arisen, and examined the expression patterns of its members and of major fibrillar collagens in the spotted catshark Scyliorhinus canicula, the thornback ray Raja clavata, and the clawed frog Xenopus tropicalis. Our phylogenetic analyses reveal that the single chondrichthyan SPARC-L gene is co-orthologous to the osteichthyan SPARC-L1 and SPARC-L2 paralogues. In all three species, odontoblasts co-express SPARC and collagens. In contrast, ameloblasts do not strongly express collagen genes but exhibit strikingly similar SPARC-L and EMP expression patterns at their maturation stage, in the examined chondrichthyan and osteichthyan species, respectively. CONCLUSIONS A well-conserved odontoblastic collagen/SPARC module across gnathostomes further confirms dentin homology. Members of the SPARC-L clade evolved faster than their SPARC paralogues, both in terms of protein sequence and gene duplication. We uncover an osteichthyan-specific duplication that produced SPARC-L1 (subsequently lost in pipidae frogs) and SPARC-L2 (independently lost in teleosts and tetrapods).Our results suggest the ameloblastic expression of the single chondrichthyan SPARC-L gene at the maturation stage reflects the ancestral gnathostome situation, and provide new evidence in favor of the homology of enamel and enameloids in all gnathostomes.
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Affiliation(s)
- Sébastien Enault
- Institut des Sciences de l’Evolution de Montpellier, ISEM, Univ Montpellier, CNRS, IRD, EPHE, Université Montpellier, UMR5554 Montpellier, France
| | - David Muñoz
- Laboratory of Development and Evolution, Department of Cell Biology, Faculty of Biological Sciences, University of Concepción, Concepción, Chile
| | - Paul Simion
- Institut des Sciences de l’Evolution de Montpellier, ISEM, Univ Montpellier, CNRS, IRD, EPHE, Université Montpellier, UMR5554 Montpellier, France
| | - Stéphanie Ventéo
- Institute for Neurosciences of Montpellier, Institut National de la Santé et de la Recherche Médicale, U1051 Montpellier, France
| | - Jean-Yves Sire
- Institut de Biologie Paris-Seine, Université Pierre et Marie Curie, UMR7138 Evolution Paris-Seine, Paris, France
| | - Sylvain Marcellini
- Laboratory of Development and Evolution, Department of Cell Biology, Faculty of Biological Sciences, University of Concepción, Concepción, Chile
| | - Mélanie Debiais-Thibaud
- Institut des Sciences de l’Evolution de Montpellier, ISEM, Univ Montpellier, CNRS, IRD, EPHE, Université Montpellier, UMR5554 Montpellier, France
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15
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Lv Y, Kawasaki K, Li J, Li Y, Bian C, Huang Y, You X, Shi Q. A Genomic Survey of SCPP Family Genes in Fishes Provides Novel Insights into the Evolution of Fish Scales. Int J Mol Sci 2017; 18:E2432. [PMID: 29144443 PMCID: PMC5713400 DOI: 10.3390/ijms18112432] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/05/2017] [Accepted: 11/14/2017] [Indexed: 11/30/2022] Open
Abstract
The family of secretory calcium-binding phosphoproteins (SCPPs) have been considered vital to skeletal tissue mineralization. However, most previous SCPP studies focused on phylogenetically distant animals but not on those closely related species. Here we provide novel insights into the coevolution of SCPP genes and fish scales in 10 species from Otophysi. According to their scale phenotypes, these fishes can be divided into three groups, i.e., scaled, sparsely scaled, and scaleless. We identified homologous SCPP genes in the genomes of these species and revealed an absence of some SCPP members in some genomes, suggesting an uneven evolutionary history of SCPP genes in fishes. In addition, most of these SCPP genes, with the exception of SPP1, individually form one or two gene cluster(s) on each corresponding genome. Furthermore, we constructed phylogenetic trees using maximum likelihood method to estimate their evolution. The phylogenetic topology mostly supports two subclasses in some species, such as Cyprinus carpio, Sinocyclocheilus anshuiensis, S. grahamin, and S. rhinocerous, but not in the other examined fishes. By comparing the gene structures of recently reported candidate genes, SCPP1 and SCPP5, for determining scale phenotypes, we found that the hypothesis is suitable for Astyanax mexicanus, but denied by S. anshuiensis, even though they are both sparsely scaled for cave adaptation. Thus, we conclude that, although different fish species display similar scale phenotypes, the underlying genetic changes however might be diverse. In summary, this paper accelerates the recognition of the SCPP family in teleosts for potential scale evolution.
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Affiliation(s)
- Yunyun Lv
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Kazuhiko Kawasaki
- Department of Anthropology, Penn State University, University Park, PA 16802, USA.
| | - Jia Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Yanping Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Yu Huang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Xinxin You
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Qiong Shi
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
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16
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Kawasaki K, Mikami M, Nakatomi M, Braasch I, Batzel P, H Postlethwait J, Sato A, Sasagawa I, Ishiyama M. SCPP Genes and Their Relatives in Gar: Rapid Expansion of Mineralization Genes in Osteichthyans. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2017. [PMID: 28643450 DOI: 10.1002/jez.b.22755] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Gar is an actinopterygian that has bone, dentin, enameloid, and ganoin (enamel) in teeth and/or scales. Mineralization of these tissues involves genes encoding various secretory calcium-binding phosphoproteins (SCPPs) in osteichthyans, but no SCPP genes have been identified in chondrichthyans to date. In the gar genome, we identified 38 SCPP genes, seven of which encode "acidic-residue-rich" proteins and 31 encode "Pro/Gln (P/Q) rich" proteins. These gar SCPP genes constitute the largest known repertoire, including many newly identified P/Q-rich genes expressed in teeth and/or scales. Among gar SCPP genes, six acidic and three P/Q-rich genes were identified as orthologs of sarcopterygian genes. The sarcopterygian orthologs of most of these acidic genes are involved in bone and/or dentin formation, and sarcopterygian orthologs of all three P/Q-rich genes participate in enamel formation. The finding of these genes in gar suggests that an elaborate SCPP gene-based genetic system for tissue mineralization was already present in stem osteichthyans. While SCPP genes have been thought to originate from ancient SPARCL1, SPARCL1L1 appears to be more closely related to these genes, because it established a structure similar to acidic SCPP genes probably in stem gnathostomes, perhaps at about the same time with the origin of tissue mineralization. Assuming enamel evolved in stem osteichthyans, all P/Q-rich SCPP genes likely arose within the osteichthyan lineage. Furthermore, the absence of acidic SCPP genes in chondrichthyans might be explained by the secondary loss of earliest acidic genes. It appears that many SCPP genes expanded rapidly in stem osteichthyans and in basal actinopterygians.
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Affiliation(s)
- Kazuhiko Kawasaki
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Masato Mikami
- Department of Microbiology, School of Life Dentistry at Niigata, The Nippon Dental University, Niigata, Japan
| | | | - Ingo Braasch
- Department of Integrative Biology and Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, Michigan
| | - Peter Batzel
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
| | | | - Akie Sato
- Department of Anatomy and Histology, School of Dental Medicine, Tsurumi University, Yokohama, Japan
| | - Ichiro Sasagawa
- Advanced Research Center, School of Life Dentistry at Niigata, The Nippon Dental University, Niigata, Japan
| | - Mikio Ishiyama
- Department of Histology, School of Life Dentistry at Niigata, The Nippon Dental University, Niigata, Japan
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17
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The seahorse genome and the evolution of its specialized morphology. Nature 2017; 540:395-399. [PMID: 27974754 PMCID: PMC8127814 DOI: 10.1038/nature20595] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 11/02/2016] [Indexed: 02/08/2023]
Abstract
Seahorses have a specialized morphology that includes a toothless tubular mouth, a body covered with bony plates, a male brood pouch, and the absence of caudal and pelvic fins. Here we report the sequencing and de novo assembly of the genome of the tiger tail seahorse, Hippocampus comes. Comparative genomic analysis identifies higher protein and nucleotide evolutionary rates in H. comes compared with other teleost fish genomes. We identified an astacin metalloprotease gene family that has undergone expansion and is highly expressed in the male brood pouch. We also find that the H. comes genome lacks enamel matrix protein-coding proline/glutamine-rich secretory calcium-binding phosphoprotein genes, which might have led to the loss of mineralized teeth. tbx4, a regulator of hindlimb development, is also not found in H. comes genome. Knockout of tbx4 in zebrafish showed a ‘pelvic fin-loss’ phenotype similar to that of seahorses. Here, the genome sequence of the tiger tail seahorse is reported and comparative genomic analyses with other ray-finned fishes are used to explore the genetic basis of the unique morphology and reproductive system of the seahorse. Seahorses are prime examples of the exuberance of evolution and are unique among bony fish on several counts, including their equine body shape and male brood pouch. An international collaboration reporting in this issue of Nature has determined the genome sequence of a seahorse (Hippocampus comes, the tiger tail seahorse). They find it to be the most rapidly evolving fish genome studied so far. H. comes is among the most commonly traded seahorse species—dried for traditional medicines and live for the aquarium trade—and is on the IUCN Red List as a 'vulnerable' species. Analysis of the genomic sequence provides insights into the evolution of its unique morphology. Of note is the absence of a master control gene, tbx4, which functions in the development of hindlimbs and pelvic fins. Pelvic fins are missing in seahorses, and tbx4-knockout mutant zebrafish also lack pelvic fins.
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18
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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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19
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Liu Z, Liu S, Yao J, Bao L, Zhang J, Li Y, Jiang C, Sun L, Wang R, Zhang Y, Zhou T, Zeng Q, Fu Q, Gao S, Li N, Koren S, Jiang Y, Zimin A, Xu P, Phillippy AM, Geng X, Song L, Sun F, Li C, Wang X, Chen A, Jin Y, Yuan Z, Yang Y, Tan S, Peatman E, Lu J, Qin Z, Dunham R, Li Z, Sonstegard T, Feng J, Danzmann RG, Schroeder S, Scheffler B, Duke MV, Ballard L, Kucuktas H, Kaltenboeck L, Liu H, Armbruster J, Xie Y, Kirby ML, Tian Y, Flanagan ME, Mu W, Waldbieser GC. The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts. Nat Commun 2016; 7:11757. [PMID: 27249958 PMCID: PMC4895719 DOI: 10.1038/ncomms11757] [Citation(s) in RCA: 182] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 04/27/2016] [Indexed: 12/31/2022] Open
Abstract
Catfish represent 12% of teleost or 6.3% of all vertebrate species, and are of enormous economic value. Here we report a high-quality reference genome sequence of channel catfish (Ictalurus punctatus), the major aquaculture species in the US. The reference genome sequence was validated by genetic mapping of 54,000 SNPs, and annotated with 26,661 predicted protein-coding genes. Through comparative analysis of genomes and transcriptomes of scaled and scaleless fish and scale regeneration experiments, we address the genomic basis for the most striking physical characteristic of catfish, the evolutionary loss of scales and provide evidence that lack of secretory calcium-binding phosphoproteins accounts for the evolutionary loss of scales in catfish. The channel catfish reference genome sequence, along with two additional genome sequences and transcriptomes of scaled catfishes, provide crucial resources for evolutionary and biological studies. This work also demonstrates the power of comparative subtraction of candidate genes for traits of structural significance.
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Affiliation(s)
- Zhanjiang Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Jun Yao
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Lisui Bao
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Jiaren Zhang
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Yun Li
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Chen Jiang
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Luyang Sun
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Ruijia Wang
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Yu Zhang
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Tao Zhou
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Qifan Zeng
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Qiang Fu
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Sen Gao
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Ning Li
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Sergey Koren
- National Center for Biodefense Analysis and Countermeasures Center, 110 Thomas Johnson Drive, Frederick, Maryland 21702, USA
| | - Yanliang Jiang
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Aleksey Zimin
- Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA
| | - Peng Xu
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Adam M Phillippy
- National Center for Biodefense Analysis and Countermeasures Center, 110 Thomas Johnson Drive, Frederick, Maryland 21702, USA
| | - Xin Geng
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Lin Song
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Fanyue Sun
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Chao Li
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Xiaozhu Wang
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Ailu Chen
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Yulin Jin
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Zihao Yuan
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Yujia Yang
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Suxu Tan
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Eric Peatman
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Jianguo Lu
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Zhenkui Qin
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Rex Dunham
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Zhaoxia Li
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Tad Sonstegard
- Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, Maryland 20705, USA
| | - Jianbin Feng
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Roy G Danzmann
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Steven Schroeder
- Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, Maryland 20705, USA
| | - Brian Scheffler
- USDA, ARS, Genomics and Bioinformatics Research Unit, P.O. Box 38, Stoneville, Mississippi 38776, USA
| | - Mary V Duke
- USDA, ARS, Genomics and Bioinformatics Research Unit, P.O. Box 38, Stoneville, Mississippi 38776, USA
| | - Linda Ballard
- USDA, ARS, Genomics and Bioinformatics Research Unit, P.O. Box 38, Stoneville, Mississippi 38776, USA
| | - Huseyin Kucuktas
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Ludmilla Kaltenboeck
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Haixia Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Jonathan Armbruster
- Department of Biological Sciences, Auburn University, Auburn, Alabama 36849, USA
| | - Yangjie Xie
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Mona L Kirby
- USDA-ARS Warmwater Aquaculture Research Unit, P.O. Box 38, 141 Experiment Station Road, Stoneville, Mississippi 38776, USA
| | - Yi Tian
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Mary Elizabeth Flanagan
- USDA-ARS Warmwater Aquaculture Research Unit, P.O. Box 38, 141 Experiment Station Road, Stoneville, Mississippi 38776, USA
| | - Weijie Mu
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA
| | - Geoffrey C Waldbieser
- USDA-ARS Warmwater Aquaculture Research Unit, P.O. Box 38, 141 Experiment Station Road, Stoneville, Mississippi 38776, USA
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20
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Sasagawa I, Oka S, Mikami M, Yokosuka H, Ishiyama M, Imai A, Shimokawa H, Uchida T. Immunohistochemical and Western Blotting Analyses of Ganoine in the Ganoid Scales ofLepisosteus oculatus: an Actinopterygian Fish. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2016; 326:193-209. [DOI: 10.1002/jez.b.22676] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 04/11/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Ichiro Sasagawa
- Advanced Research Center; School of Life Dentistry at Niigata; The Nippon Dental University; Niigata Japan
| | - Shunya Oka
- Department of Biology; School of Life Dentistry at Niigata; The Nippon Dental University; Niigata Japan
| | - Masato Mikami
- Department of Microbiology; School of Life Dentistry at Niigata; The Nippon Dental University; Niigata Japan
| | - Hiroyuki Yokosuka
- Department of Histology; School of Life Dentistry at Niigata; The Nippon Dental University; Niigata Japan
| | - Mikio Ishiyama
- Department of Histology; School of Life Dentistry at Niigata; The Nippon Dental University; Niigata Japan
| | - Akane Imai
- Department of Biochemistry, School of Life Dentistry at Niigata; The Nippon Dental University; Niigata Japan
- Department of Dental Hygiene, College at Niigata; The Nippon Dental University; Niigata Japan
| | - Hitoyata Shimokawa
- Division of Pediatric Dentistry, Department of Oral Health Sciences, Graduate School; Tokyo Medical and Dental University; Bunkyo-ku, Tokyo Japan
| | - Takashi Uchida
- Department of Oral Biology, Graduate School of Biomedical Sciences; Hiroshima University; Hiroshima Japan
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21
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Núñez SM, Chun YHP, Ganss B, Hu Y, Richardson AS, Schmitz JE, Fajardo R, Yang J, Hu JCC, Simmer JP. Maturation stage enamel malformations in Amtn and Klk4 null mice. Matrix Biol 2016; 52-54:219-233. [PMID: 26620968 PMCID: PMC4875837 DOI: 10.1016/j.matbio.2015.11.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 11/20/2015] [Accepted: 11/23/2015] [Indexed: 12/14/2022]
Abstract
Amelotin (AMTN) and kallikrein-4 (KLK4) are secreted proteins specialized for enamel biomineralization. We characterized enamel from wild-type, Amtn(-/-), Klk4(-/-), Amtn(+/-)Klk4(+/-) and Amtn(-/-)Klk4(-/-) mice to gain insights into AMTN and KLK4 functions during amelogenesis. All of the null mice were healthy and fertile. The mandibular incisors in Amtn(-/-), Klk4(-/-) and Amtn(-/-)Klk4(-/-) mice were chalky-white and chipped. No abnormalities except in enamel were observed, and no significant differences were detected in enamel thickness or volume, or in rod decussation. Micro-computed tomography (μCT) maximum intensity projections localized the onset of enamel maturation in wild-type incisors distal to the first molar, but mesial to this position in Amtn(-/-), Klk4(-/-) and Amtn(-/-)Klk4(-/-) mice, demonstrating a delay in enamel maturation in Amtn(-/-) incisors. Micro-CT detected significantly reduced enamel mineral density (2.5 and 2.4gHA/cm(3)) in the Klk4(-/-) and Amtn(-/-)Klk4(-/-) mice respectively, compared with wild-type enamel (3.1gHA/cm(3)). Backscatter scanning electron microscopy showed that mineral density progressively diminished with enamel depth in the Klk4(-/-) and Amtn(-/-)Klk4(-/-) mice. The Knoop hardness of the Amtn(-/-) outer enamel was significantly reduced relative to the wild-type and was not as hard as the middle or inner enamel. Klk4(-/-) enamel hardness was significantly reduced at all levels, but the outer enamel was significantly harder than the inner and middle enamel. Thus the hardness patterns of the Amtn(-/-) and Klk4(-/-) mice were distinctly different, while the Amtn(-/-)Klk4(-/-) outer enamel was not as hard as in the Amtn(-/-) and Klk4(-/-) mice. We conclude that AMTN and KLK4 function independently, but are both necessary for proper enamel maturation.
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Affiliation(s)
- Stephanie M Núñez
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, 1210 Eisenhower Pl., Ann Arbor, MI, USA 48108.
| | - Yong-Hee P Chun
- Department of Periodontics, School of Dentistry, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr., San Antonio, TX 78240, USA.
| | - Bernhard Ganss
- Matrix Dynamics Group, Faculty of Dentistry, University of Toronto, 150 College Street, Fitzgerald Building, Toronto, ON M5S 3E2, Canada.
| | - Yuanyuan Hu
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, 1210 Eisenhower Pl., Ann Arbor, MI, USA 48108.
| | - Amelia S Richardson
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, 1210 Eisenhower Pl., Ann Arbor, MI, USA 48108.
| | - James E Schmitz
- Department of Orthopaedics, RAYO, Carlisle Center for Bone and Mineral Imaging, School of Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr., San Antonio, TX, USA.
| | - Roberto Fajardo
- Department of Orthopaedics, RAYO, Carlisle Center for Bone and Mineral Imaging, School of Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr., San Antonio, TX, USA.
| | - Jie Yang
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, 1210 Eisenhower Pl., Ann Arbor, MI, USA 48108; Department of Pediatric Dentistry, School and Hospital of Stomatology, Peking University, 22 South Avenue, Zhongguancun Haidian District, Beijing 100081, PR China.
| | - Jan C-C Hu
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, 1210 Eisenhower Pl., Ann Arbor, MI, USA 48108.
| | - James P Simmer
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, 1210 Eisenhower Pl., Ann Arbor, MI, USA 48108.
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22
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Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, Ravi V, Lee AP, Nakamura T, Chalopin D, Fan S, Wcisel D, Cañestro C, Sydes J, Beaudry FEG, Sun Y, Hertel J, Beam MJ, Fasold M, Ishiyama M, Johnson J, Kehr S, Lara M, Letaw JH, Litman GW, Litman RT, Mikami M, Ota T, Saha NR, Williams L, Stadler PF, Wang H, Taylor JS, Fontenot Q, Ferrara A, Searle SMJ, Aken B, Yandell M, Schneider I, Yoder JA, Volff JN, Meyer A, Amemiya CT, Venkatesh B, Holland PWH, Guiguen Y, Bobe J, Shubin NH, Di Palma F, Alföldi J, Lindblad-Toh K, Postlethwait JH. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nat Genet 2016; 48:427-37. [PMID: 26950095 PMCID: PMC4817229 DOI: 10.1038/ng.3526] [Citation(s) in RCA: 403] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 02/12/2016] [Indexed: 12/16/2022]
Abstract
To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.
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Affiliation(s)
- Ingo Braasch
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Andrew R Gehrke
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, USA
| | - Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, Kentucky, USA
| | - Kazuhiko Kawasaki
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Tereza Manousaki
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Jeremy Pasquier
- Institut National de la Recherche Agronomique (INRA), UR1037 Laboratoire de Physiologie et Génomique des Poissons (LPGP), Campus de Beaulieu, Rennes, France
| | - Angel Amores
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Peter Batzel
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Julian Catchen
- Department of Animal Biology, University of Illinois, Urbana-Champaign, Illinois, USA
| | - Aaron M Berlin
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael S Campbell
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Daniel Barrell
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Kyle J Martin
- Department of Zoology, University of Oxford, Oxford, UK
| | - John F Mulley
- School of Biological Sciences, Bangor University, Bangor, UK
| | - Vydianathan Ravi
- Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Alison P Lee
- Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Tetsuya Nakamura
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, USA
| | - Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Shaohua Fan
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Dustin Wcisel
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina, USA
| | - Cristian Cañestro
- Departament de Genètica, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
| | - Jason Sydes
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Felix E G Beaudry
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Yi Sun
- Center for Circadian Clocks, Soochow University, Suzhou, China
- School of Biology and Basic Medical Sciences, Medical College, Soochow University, Suzhou, China
| | - Jana Hertel
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Michael J Beam
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Mario Fasold
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Mikio Ishiyama
- Department of Dental Hygiene, Nippon Dental University College at Niigata, Niigata, Japan
| | - Jeremy Johnson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Steffi Kehr
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Marcia Lara
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - John H Letaw
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Gary W Litman
- Department of Pediatrics, University of South Florida Morsani College of Medicine, St. Petersburg, Florida, USA
| | - Ronda T Litman
- Department of Pediatrics, University of South Florida Morsani College of Medicine, St. Petersburg, Florida, USA
| | - Masato Mikami
- Department of Microbiology, Nippon Dental University School of Life Dentistry at Niigata, Niigata, Japan
| | - Tatsuya Ota
- Department of Evolutionary Studies of Biosystems, SOKENDAI (Graduate University for Advanced Studies), Hayama, Japan
| | - Nil Ratan Saha
- Molecular Genetics Program, Benaroya Research Institute, Seattle, Washington, USA
| | - Louise Williams
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Han Wang
- Center for Circadian Clocks, Soochow University, Suzhou, China
- School of Biology and Basic Medical Sciences, Medical College, Soochow University, Suzhou, China
| | - John S Taylor
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Quenton Fontenot
- Department of Biological Sciences, Nicholls State University, Thibodaux, Louisiana, USA
| | - Allyse Ferrara
- Department of Biological Sciences, Nicholls State University, Thibodaux, Louisiana, USA
| | - Stephen M J Searle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Bronwen Aken
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Mark Yandell
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Igor Schneider
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem, Brazil
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina, USA
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
- International Max Planck Research School for Organismal Biology, University of Konstanz, Konstanz, Germany
| | - Chris T Amemiya
- Molecular Genetics Program, Benaroya Research Institute, Seattle, Washington, USA
| | - Byrappa Venkatesh
- Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | | | - Yann Guiguen
- Institut National de la Recherche Agronomique (INRA), UR1037 Laboratoire de Physiologie et Génomique des Poissons (LPGP), Campus de Beaulieu, Rennes, France
| | - Julien Bobe
- Institut National de la Recherche Agronomique (INRA), UR1037 Laboratoire de Physiologie et Génomique des Poissons (LPGP), Campus de Beaulieu, Rennes, France
| | - Neil H Shubin
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, USA
| | | | - Jessica Alföldi
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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23
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Abstract
Teleosts have emerged as important model organisms, yet their ancestrally duplicated genomes sometimes complicate developmental genetic analyses and comparisons to humans. A new genome sequence of spotted gar, a fish related to teleosts but lacking a duplicated genome, now helps to bridge human and teleost biology.
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Affiliation(s)
- David M Parichy
- Department of Biology, University of Washington, Seattle, Washington, USA
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24
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Yang J, Kawasaki K, Lee M, Reid BM, Nunez SM, Choi M, Seymen F, Koruyucu M, Kasimoglu Y, Estrella-Yuson N, Lin BPJ, Simmer JP, Hu JCC. The dentin phosphoprotein repeat region and inherited defects of dentin. Mol Genet Genomic Med 2016; 4:28-38. [PMID: 26788535 PMCID: PMC4707025 DOI: 10.1002/mgg3.176] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/05/2015] [Accepted: 08/06/2015] [Indexed: 11/12/2022] Open
Abstract
Nonsyndromic dentin defects classified as type II dentin dysplasia and types II and III dentinogenesis imperfecta are caused by mutations in DSPP (dentin sialophosphoprotein). Most reported disease‐causing DSPP mutations occur within the repetitive DPP (dentin phosphoprotein) coding sequence. We characterized the DPP sequences of five probands with inherited dentin defects using single molecule real‐time (SMRT) DNA sequencing. Eight of the 10 sequences matched previously reported DPP length haplotypes and two were novel. Alignment with known DPP sequences showed 32 indels arranged in 36 different patterns. Sixteen of the 32 indels were not represented in more than one haplotype. The 25 haplotypes with confirmed indels were aligned to generate a tree that describes how the length variations might have evolved. Some indels were independently generated in multiple lines. A previously reported disease‐causing DSPP mutation in Family 1 was confirmed and its position clarified (c.3135delC; p.Ser1045Argfs*269). A novel frameshift mutation (c.3504_3508dup; p.Asp1170Alafs*146) caused the dentin defects in Family 2. A COL1A2 (c.2027G>A or p.Gly676Asp) missense mutation, discovered by whole‐exome sequencing, caused the dentin defects in Family 3. We conclude that SMRT sequencing characterizes the DPP repeat region without cloning and can improve our understanding of normal and pathological length variations in DSPP alleles.
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Affiliation(s)
- Jie Yang
- Department of Biologic and Materials SciencesUniversity of Michigan School of Dentistry1210 Eisenhower PlaceAnn ArborMichigan; Department of Pediatric DentistrySchool and Hospital of StomatologyPeking University22 South AvenueZhongguancun Haidian DistrictBeijing100081China
| | - Kazuhiko Kawasaki
- Department of Anthropology Pennsylvania State University University Park Pennsylvania 16802
| | - Moses Lee
- Department of Biomedical Sciences Seoul National University College of Medicine 275-1 Yongon-dong, Chongno-gu Seoul 110-768 Korea
| | - Bryan M Reid
- Department of Biologic and Materials Sciences University of Michigan School of Dentistry 1210 Eisenhower Place Ann Arbor Michigan
| | - Stephanie M Nunez
- Department of Biologic and Materials Sciences University of Michigan School of Dentistry 1210 Eisenhower Place Ann Arbor Michigan
| | - Murim Choi
- Department of Biomedical Sciences Seoul National University College of Medicine 275-1 Yongon-dong, Chongno-gu Seoul 110-768 Korea
| | - Figen Seymen
- Department of Pedodontics Faculty of Dentistry Istanbul University Istanbul Turkey
| | - Mine Koruyucu
- Department of Pedodontics Faculty of Dentistry Istanbul University Istanbul Turkey
| | - Yelda Kasimoglu
- Department of Pedodontics Faculty of Dentistry Istanbul University Istanbul Turkey
| | - Ninna Estrella-Yuson
- Department of Paediatric Dentistry Women's and Children's Hospital 72 King William Road North Adelaide South Australia 5006 Australia
| | - Brent P J Lin
- Department of Pediatric Dentistry School of Dentistry University of California San Francisco California
| | - James P Simmer
- Department of Biologic and Materials Sciences University of Michigan School of Dentistry 1210 Eisenhower Place Ann Arbor Michigan
| | - Jan C-C Hu
- Department of Biologic and Materials Sciences University of Michigan School of Dentistry 1210 Eisenhower Place Ann Arbor Michigan
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Hu Y, Smith CE, Richardson AS, Bartlett JD, Hu JCC, Simmer JP. MMP20, KLK4, and MMP20/KLK4 double null mice define roles for matrix proteases during dental enamel formation. Mol Genet Genomic Med 2015; 4:178-96. [PMID: 27066511 PMCID: PMC4799876 DOI: 10.1002/mgg3.194] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 11/12/2015] [Accepted: 11/13/2015] [Indexed: 01/08/2023] Open
Abstract
Matrix metalloproteinase 20 (MMP20) and kallikrein‐related peptidase 4 (KLK4) are secreted proteinases that are essential for proper dental enamel formation. We characterized and compared enamel formed in wild‐type, Mmp20−/−, Klk4−/−, Mmp20+/−Klk4+/−, and Mmp20−/−Klk4−/− mice using dissecting and light microscopy, backscattered scanning electron microscopy (bSEM), SEM, microcomputed tomography (μCT), and energy‐dispersive X‐ray analysis (EDX). Following eruption, fractures were observed on Mmp20−/−, Klk4−/−, Mmp20+/−Klk4+/−, and Mmp20−/−Klk4−/− molars. Failure of the enamel in the Mmp20+/−Klk4+/− molars was unexpected and suggested that digenic effects could contribute to the etiology of amelogenesis imperfecta in humans. Micro‐CT analyses of hemimandibles demonstrated significantly reduced high‐density enamel volume in the Mmp20−/− and Klk4−/− mice relative to the wild‐type, which was further reduced in Mmp20−/−Klk4−/− mice. bSEM images of 7‐week Mmp20−/− and Mmp20−/−Klk4−/− mandibular incisors showed rough, pitted enamel surfaces with numerous indentations and protruding nodules. The Mmp20+/− and Mmp20+/−Klk4+/− incisors showed prominent, evenly spaced, horizontal ridges that were more distinct in Mmp20+/−Klk4+/− incisors relative to Mmp20+/− incisors due to the darkening of the valleys between the ridges. In cross sections, the Mmp20−/− and Mmp20−/−Klk4−/− exhibited three distinct layers. The outer layer exhibited a disturbed elemental composition and an irregular enamel surface covered with nodules. The Mmp20 null enamel was apparently unable to withstand the sheer forces associated with eruption and separated from dentin during development. Cells invaded the cracks and interposed between the dentin and enamel layers. MMP20 and KLK4 serve overlapping and complementary functions to harden enamel by removing protein, but MMP20 potentially serves multiple additional functions necessary for the adherence of enamel to dentin, the release of intercellular protein stores into the enamel matrix, the retreat of ameloblasts to facilitate thickening of the enamel layer, and the timely transition of ameloblasts to maturation.
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Affiliation(s)
- Yuanyuan Hu
- Departments of Biologic and Materials Sciences University of Michigan School of Dentistry 1210 Eisenhower Place Ann Arbor Michigan 48108
| | - Charles E Smith
- Departments of Biologic and Materials SciencesUniversity of Michigan School of Dentistry1210 Eisenhower PlaceAnn ArborMichigan48108; Facility for Electron Microscopy ResearchDepartment of Anatomy and Cell Biology and Faculty of DentistryMcGill UniversityMontrealQuebecH3A 2B2Canada
| | - Amelia S Richardson
- Departments of Biologic and Materials Sciences University of Michigan School of Dentistry 1210 Eisenhower Place Ann Arbor Michigan 48108
| | - John D Bartlett
- Office of Research College of Dentistry Ohio State University 4139 Postle Hall, 305 W. 12th Ave. Columbus Ohio 43210
| | - Jan C C Hu
- Departments of Biologic and Materials Sciences University of Michigan School of Dentistry 1210 Eisenhower Place Ann Arbor Michigan 48108
| | - James P Simmer
- Departments of Biologic and Materials Sciences University of Michigan School of Dentistry 1210 Eisenhower Place Ann Arbor Michigan 48108
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Gasse B, Sire JY. Comparative expression of the four enamel matrix protein genes, amelogenin, ameloblastin, enamelin and amelotin during amelogenesis in the lizard Anolis carolinensis. EvoDevo 2015; 6:29. [PMID: 26421144 PMCID: PMC4587831 DOI: 10.1186/s13227-015-0024-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 09/15/2015] [Indexed: 12/23/2022] Open
Abstract
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.
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Affiliation(s)
- Barbara Gasse
- UMR7138, Institut de Biologie Paris-Seine (IBPS), UPMC Univ Paris 06, Sorbonne Universités, 75005 Paris, France
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Mineral homeostasis and regulation of mineralization processes in the skeletons of sharks, rays and relatives (Elasmobranchii). Semin Cell Dev Biol 2015; 46:51-67. [DOI: 10.1016/j.semcdb.2015.10.022] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/13/2015] [Indexed: 01/01/2023]
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New genomic and fossil data illuminate the origin of enamel. Nature 2015; 526:108-11. [PMID: 26416752 DOI: 10.1038/nature15259] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 07/28/2015] [Indexed: 12/20/2022]
Abstract
Enamel, the hardest vertebrate tissue, covers the teeth of almost all sarcopterygians (lobe-finned bony fishes and tetrapods) as well as the scales and dermal bones of many fossil lobe-fins. Enamel deposition requires an organic matrix containing the unique enamel matrix proteins (EMPs) amelogenin (AMEL), enamelin (ENAM) and ameloblastin (AMBN). Chondrichthyans (cartilaginous fishes) lack both enamel and EMP genes. Many fossil and a few living non-teleost actinopterygians (ray-finned bony fishes) such as the gar, Lepisosteus, have scales and dermal bones covered with a proposed enamel homologue called ganoine. However, no gene or transcript data for EMPs have been described from actinopterygians. Here we show that Psarolepis romeri, a bony fish from the the Early Devonian period, combines enamel-covered dermal odontodes on scales and skull bones with teeth of naked dentine, and that Lepisosteus oculatus (the spotted gar) has enam and ambn genes that are expressed in the skin, probably associated with ganoine formation. The genetic evidence strengthens the hypothesis that ganoine is homologous with enamel. The fossil evidence, further supported by the Silurian bony fish Andreolepis, which has enamel-covered scales but teeth and odontodes on its dermal bones made of naked dentine, indicates that this tissue originated on the dermal skeleton, probably on the scales. It subsequently underwent heterotopic expansion across two highly conserved patterning boundaries (scales/head-shoulder and dermal/oral) within the odontode skeleton.
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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, Liu X, Corre E, Sire JY. Amelotin Gene Structure and Expression during Enamel Formation in the Opossum Monodelphis domestica. PLoS One 2015; 10:e0133314. [PMID: 26186457 PMCID: PMC4506066 DOI: 10.1371/journal.pone.0133314] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/24/2015] [Indexed: 11/23/2022] Open
Abstract
Amelotin (AMTN) is an ameloblast-secreted protein that belongs to the secretory calcium-binding phosphoprotein family, which also includes the enamel matrix proteins amelogenin, ameloblastin and enamelin. Although AMTN is supposed to play an important role in enamel formation, data were long limited to the rodents, in which it is expressed during the maturation stage. Recent comparative studies in sauropsids and amphibians revealed that (i) AMTN was expressed earlier, i.e. as soon as ameloblasts are depositing the enamel matrix, and (ii) AMTN structure was different, a change which mostly resulted from an intraexonic splicing in the large exon 8 of an ancestral mammal. The present study was performed to know whether the differences in AMTN structure and expression in rodents compared to non-mammalian tetrapods dated back to an early ancestral mammal or were acquired later in mammalian evolution. We sequenced, assembled and screened the jaw transcriptome of a neonate opossum Monodelphis domestica, a marsupial. We found two AMTN transcripts. Variant 1, representing 70.8% of AMTN transcripts, displayed the structure known in rodents, whereas variant 2 (29.2%) exhibited the nonmammalian tetrapod structure. Then, we studied AMTN expression during amelogenesis in a neonate specimen. We obtained similar data as those reported in rodents. These findings indicate that more than 180 million years ago, before the divergence of marsupials and placentals, changes occurred in AMTN function and structure. The spatiotemporal expression was delayed to the maturation stage of amelogenesis and the intraexonic splicing gave rise to isoform 1, encoded by variant 1 and lacking the RGD motif. The ancestral isoform 2, housing the RGD, was initially conserved, as demonstrated here in a marsupial, then secondarily lost in the placental lineages. These findings bring new elements towards our understanding of the non-prismatic to prismatic enamel transition that occurred at the onset of mammals.
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Affiliation(s)
- Barbara Gasse
- Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), UMR7138, 75005 Paris, France
- CNRS, IBPS, UMR7138, 75005 Paris, France
| | - Xi Liu
- Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), UMR7138, 75005 Paris, France
- CNRS, IBPS, UMR7138, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, Plateforme ABiMS (Analyses and Bioinformatics for Marine Science), 29680 Roscoff, France
| | - Erwan Corre
- Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, Plateforme ABiMS (Analyses and Bioinformatics for Marine Science), 29680 Roscoff, France
| | - Jean-Yves Sire
- Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), UMR7138, 75005 Paris, France
- CNRS, IBPS, UMR7138, 75005 Paris, France
- * E-mail:
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Kawasaki K, Hu JCC, Simmer JP. Evolution of Klk4 and enamel maturation in eutherians. Biol Chem 2015; 395:1003-13. [PMID: 25153384 DOI: 10.1515/hsz-2014-0122] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 06/09/2014] [Indexed: 12/23/2022]
Abstract
Kallikrein-related peptidase 4 (KLK4) is a secreted serine protease that degrades residual enamel proteins to facilitate their removal by ameloblasts, which increases mineralization and hardens the enamel. Mutations in human KLK4 cause hypomaturation amelogenesis imperfecta. Enamel formed by Klk4 null mice is normal in thickness and prism structure, but the enamel layer retains proteins, is hypomineralized, and undergoes rapid attrition following tooth eruption. We searched multiple databases, retrieved Klk4 and Klk5 from various mammalian genomes, and identified Klk4 in 46 boreoeutherian genomes. In non-Boreoeutheria, Klk4 was detected in only one afrotherian genome (as a pseudogene), and not in the other six afrotherian, two xenarthran, or three marsupial genomes. In contrast, Klk5 was detected in both marsupial and eutherian mammals. Our phylogenetic and mutation rate analyses support the hypothesis that Klk4 arose from Klk5 by gene duplication near the divergence of Afrotheria, Xenarthra and Boreoeutheria, and that functionally-differentiated Klk4 survived only in Boreoeutheria. Afrotherian mammals share the feature of delayed dental eruption relative to boreoeutherian mammals. KLK4 shortens the time required for enamel maturation and could have alleviated negative selection following mutations that resulted in thicker enamel or earlier tooth eruption, without reducing enamel hardness or causing dental attrition.
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Gasse B, Chiari Y, Silvent J, Davit-Béal T, Sire JY. Amelotin: an enamel matrix protein that experienced distinct evolutionary histories in amphibians, sauropsids and mammals. BMC Evol Biol 2015; 15:47. [PMID: 25884299 PMCID: PMC4373244 DOI: 10.1186/s12862-015-0329-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 02/24/2015] [Indexed: 01/21/2023] Open
Abstract
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.
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Affiliation(s)
- Barbara Gasse
- Institut de Biologie Paris-Seine, Université Pierre et Marie Curie, Evolution Paris-Seine, Paris, UMR7138, France.
| | - Ylenia Chiari
- Department of Biology, University of South Alabama, Mobile, AL, 36688, USA.
| | - Jérémie Silvent
- Institut de Biologie Paris-Seine, Université Pierre et Marie Curie, Evolution Paris-Seine, Paris, UMR7138, France. .,Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel.
| | - Tiphaine Davit-Béal
- Institut de Biologie Paris-Seine, Université Pierre et Marie Curie, Evolution Paris-Seine, Paris, UMR7138, France.
| | - Jean-Yves Sire
- Institut de Biologie Paris-Seine, Université Pierre et Marie Curie, Evolution Paris-Seine, Paris, UMR7138, France.
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Affiliation(s)
- J D Bartlett
- Department of Mineralized Tissue Biology, The Forsyth Institute, Cambridge, MA, USA
| | - J P Simmer
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, Ann Arbor, MI, USA
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