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Randall JG, Gatesy J, McGowen MR, Springer MS. Molecular Evidence for Relaxed Selection on the Enamel Genes of Toothed Whales (Odontoceti) with Degenerative Enamel Phenotypes. Genes (Basel) 2024; 15:228. [PMID: 38397217 PMCID: PMC10888366 DOI: 10.3390/genes15020228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Different species of toothed whales (Odontoceti) exhibit a variety of tooth forms and enamel types. Some odontocetes have highly prismatic enamel with Hunter-Schreger bands, whereas enamel is vestigial or entirely lacking in other species. Different tooth forms and enamel types are associated with alternate feeding strategies that range from biting and grasping prey with teeth in most oceanic and river dolphins to the suction feeding of softer prey items without the use of teeth in many beaked whales. At the molecular level, previous studies have documented inactivating mutations in the enamel-specific genes of some odontocete species that lack complex enamel. At a broader scale, however, it is unclear whether enamel complexity across the full diversity of extant Odontoceti correlates with the relative strength of purifying selection on enamel-specific genes. Here, we employ sequence alignments for seven enamel-specific genes (ACP4, AMBN, AMELX, AMTN, ENAM, KLK4, MMP20) in 62 odontocete species that are representative of all extant families. The sequences for 33 odontocete species were obtained from databases, and sequences for the remaining 29 species were newly generated for this study. We screened these alignments for inactivating mutations (e.g., frameshift indels) and provide a comprehensive catalog of these mutations in species with one or more inactivated enamel genes. Inactivating mutations are rare in Delphinidae (oceanic dolphins) and Platanistidae/Inioidea (river dolphins) that have higher enamel complexity scores. By contrast, mutations are much more numerous in clades such as Monodontidae (narwhal, beluga), Ziphiidae (beaked whales), Physeteroidea (sperm whales), and Phocoenidae (porpoises) that are characterized by simpler enamel or even enamelless teeth. Further, several higher-level taxa (e.g., Hyperoodon, Kogiidae, Monodontidae) possess shared inactivating mutations in one or more enamel genes, which suggests loss of function of these genes in the common ancestor of each clade. We also performed selection (dN/dS) analyses on a concatenation of these genes and used linear regression and Spearman's rank-order correlation to test for correlations between enamel complexity and two different measures of selection intensity (# of inactivating mutations per million years, dN/dS values). Selection analyses revealed that relaxed purifying selection is especially prominent in physeteroids, monodontids, and phocoenids. Linear regressions and correlation analyses revealed a strong negative correlation between selective pressure (dN/dS values) and enamel complexity. Stronger purifying selection (low dN/dS) is found on branches with more complex enamel and weaker purifying selection (higher dN/dS) occurs on branches with less complex enamel or enamelless teeth. As odontocetes diversified into a variety of feeding modes, in particular, the suction capture of prey, a reduced reliance on the dentition for prey capture resulted in the relaxed selection of genes that are critical to enamel development.
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Affiliation(s)
- Jason G. Randall
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA;
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA;
| | - Michael R. McGowen
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, MRC 108, P.O. Box 37012, Washington, DC 20013, USA;
| | - Mark S. Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA;
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Anatomical, Ontogenetic, and Genomic Homologies Guide Reconstructions of the Teeth-to-Baleen Transition in Mysticete Whales. J MAMM EVOL 2022. [DOI: 10.1007/s10914-022-09614-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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3
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Randall JG, Gatesy J, Springer MS. Molecular evolutionary analyses of tooth genes support sequential loss of enamel and teeth in baleen whales (Mysticeti). Mol Phylogenet Evol 2022; 171:107463. [PMID: 35358696 DOI: 10.1016/j.ympev.2022.107463] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/16/2021] [Accepted: 03/01/2022] [Indexed: 10/18/2022]
Abstract
The loss of teeth and evolution of baleen racks in Mysticeti was a profound transformation that permitted baleen whales to radiate and diversify into a previously underutilized ecological niche of bulk filter-feeding on zooplankton and other small prey. Ancestral state reconstructions suggest that postnatal teeth were lost in the common ancestor of crown Mysticeti. Genomic studies provide some support for this hypothesis and suggest that the genetic toolkit for enamel production was inactivated in the common ancestor of living baleen whales. However, molecular studies to date have not provided direct evidence for the complete loss of teeth, including their dentin component, on the stem mysticete branch. Given these results, several questions remain unanswered: (1) Were teeth lost in a single step or did enamel loss precede dentin loss? (2) Was enamel lost early or late on the stem mysticete branch? (3) If enamel and dentin/tooth loss were decoupled in the ancestry of baleen whales, did dentin loss occur on the stem mysticete branch or independently in different crown mysticete lineages? To address these outstanding questions, we compiled and analyzed complete protein-coding sequences for nine tooth-related genes from cetaceans with available genome data. Seven of these genes are associated with enamel formation (ACP4, AMBN, AMELX, AMTN, ENAM, KLK4, MMP20) whereas two other genes are either dentin-specific (DSPP) or tooth-specific (ODAPH) but not enamel-specific. Molecular evolutionary analyses indicate that all seven enamel-specific genes have inactivating mutations that are scattered across branches of the mysticete tree. Three of the enamel genes (ACP4, KLK4, MMP20) have inactivating mutations that are shared by all mysticetes. The two genes that are dentin-specific (DSPP) or tooth-specific (ODAPH) do not have any inactivating mutations that are shared by all mysticetes, but there are shared mutations in Balaenidae as well as in Plicogulae (Neobalaenidae + Balaenopteroidea). These shared mutations suggest that teeth were lost at most two times. Shared inactivating mutations and dN/dS analyses, in combination with cetacean divergence times, were used to estimate inactivation times of genes and by proxy enamel and tooth phenotypes at ancestral nodes. The results of these analyses are most compatible with a two-step model for the loss of teeth in the ancestry of living baleen whales: enamel was lost very early on the stem Mysticeti branch followed by the independent loss of dentin (and teeth) in the common ancestors of Balaenidae and Plicogulae, respectively. These results imply that some stem mysticetes, and even early crown mysticetes, may have had vestigial teeth comprised of dentin with no enamel. Our results also demonstrate that all odontocete species (in our study) with absent or degenerative enamel have inactivating mutations in one or more of their enamel genes.
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Affiliation(s)
- Jason G Randall
- Department of Evolution, Ecology, and Evolutionary Biology, University of California, Riverside, CA 92521, USA.
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA.
| | - Mark S Springer
- Department of Evolution, Ecology, and Evolutionary Biology, University of California, Riverside, CA 92521, USA.
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4
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Molecular Evolution of Tooth-Related Genes Provides New Insights into Dietary Adaptations of Mammals. J Mol Evol 2021; 89:458-471. [PMID: 34287664 PMCID: PMC8318974 DOI: 10.1007/s00239-021-10017-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 06/10/2021] [Indexed: 11/01/2022]
Abstract
Mammals have evolved different tooth phenotypes that are hypothesized to be associated with feeding habits. However, the genetic basis for the linkage has not been well explored. In this study, we investigated 13 tooth-related genes, including seven enamel-related genes (AMELX, AMBN, ENAM, AMTN, ODAM, KLK4 and MMP20) and six dentin-related genes (DSPP, COL1A1, DMP1, IBSP, MEPE and SPP1), from 63 mammals to determine their evolutionary history. Our results showed that different evolutionary histories have evolved among divergent feeding habits in mammals. There was stronger positive selection for eight genes (ENAM, AMTN, ODAM, KLK4, DSPP, DMP1, COL1A1, MEPE) in herbivore lineages. In addition, AMELX, AMBN, ENAM, AMTN, MMP20 and COL1A1 underwent accelerated evolution in herbivores. While relatively strong positive selection was detected in IBSP, SPP1, and DSPP, accelerated evolution was only detected for MEPE and SPP1 genes among the carnivorous lineages. We found positive selection on AMBN and ENAM genes for omnivorous primates in the catarrhini clade. Interestingly, a significantly positive association between the evolutionary rate of ENAM, ODAM, KLK4, MMP20 and the average enamel thickness was found in primates. Additionally, we found molecular convergence in some amino acid sites of tooth-related genes among the lineages whose feeding habit are similar. The positive selection of related genes might promote the formation and bio-mineralization of tooth enamel and dentin, which would make the tooth structure stronger. Our results revealed that mammalian tooth-related genes have experienced variable evolutionary histories, which provide some new insights into the molecular basis of dietary adaptation in mammals.
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Patterns and tempo of PCSK9 pseudogenizations suggest an ancient divergence in mammalian cholesterol homeostasis mechanisms. Genetica 2021; 149:1-19. [PMID: 33515402 PMCID: PMC7929951 DOI: 10.1007/s10709-021-00113-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 01/04/2021] [Indexed: 01/06/2023]
Abstract
Proprotein convertase subtilisin/kexin type 9 (PCSK9) plays a central role in cholesterol homeostasis in humans as a major regulator of LDLR levels. PCSK9 is an intriguing protease in that it does not act by proteolysis but by preventing LDLR recirculation from endosomes to the plasma membrane. This, and the inexistence of any other proteolytic substrate but itself could suggest that PCSK9 is an exquisite example of evolutionary fine-tuning. However, the gene has been lost in several mammalian species, and null alleles are present (albeit at low frequencies) in some human populations without apparently deleterious health effects, raising the possibility that the PCSK9 may have become dispensable in the mammalian lineage. To address this issue, we systematically recovered, assembled, corrected, annotated and analysed publicly available PCSK9 sequences for 420 eutherian species to determine the distribution, frequencies, mechanisms and timing of PCSK9 pseudogenization events, as well as the evolutionary pressures underlying the preservation or loss of the gene. We found a dramatic difference in the patterns of PCSK9 retention and loss between Euarchontoglires—where there is strong pressure for gene preservation—and Laurasiatheria, where multiple independent events have led to PCSK9 loss in most species. These results suggest that there is a fundamental difference in the regulation of cholesterol metabolism between Euarchontoglires and Laurasiatheria, which in turn has important implications for the use of Laurasiatheria species (e.g. pigs) as animal models of human cholesterol-related diseases.
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6
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Mu Y, Huang X, Liu R, Gai Y, Liang N, Yin D, Shan L, Xu S, Yang G. ACPT gene is inactivated in mammalian lineages that lack enamel or teeth. PeerJ 2021; 9:e10219. [PMID: 33552707 PMCID: PMC7831365 DOI: 10.7717/peerj.10219] [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: 04/06/2020] [Accepted: 09/29/2020] [Indexed: 12/31/2022] Open
Abstract
Loss of tooth or enamel is widespread in multiple mammal lineages. Although several studies have been reported, the evolutionary mechanisms of tooth/enamel loss are still unclear. Most previous studies have found that some tooth-related genes have been inactivated in toothless and/or enamel-less mammals, such as ENAM, ODAM, C4orf26, AMBN, AMTN, DSPP, etc. Here, we conducted evolutionary analyses on ACPT playing a key role in amelogenesis, to interrogate the mechanisms. We obtained the ACPT sequences from 116 species, including edentulous and enamel-less mammals. The results shows that variant ORF-disrupting mutations were detected in ACPT coding region among nine edentulous baleen whales and three enamel-less taxa (pygmy sperm whale, aardvark, nine-banded armadillo). Furtherly, selective pressure uncovered that the selective constraints have been relaxed among all toothless and enamel-less lineages. Moreover, our results support the hypothesis that mineralized teeth were lost or degenerated in the common ancestor of crown Mysticeti through two shared single-base sites deletion in exon 4 and 5 of ACPT among all living baleen whales. DN/dS values on transitional branches were used to estimate ACPT inactivation records. In the case of aardvark, inactivation of ACPT was estimated at ~23.60–28.32 Ma, which is earlier than oldest aardvark fossil record (Orycteropus minutus, ~19 Ma), suggesting that ACPT inactivation may result in degeneration or loss of enamel. Conversely, the inactivation time of ACPT estimated in armadillo (~10.18–11.30 Ma) is later than oldest fossil record, suggesting that inactivation of ACPT may result from degeneration or loss of enamel in these mammals. Our findings suggested that different mechanisms of degeneration of tooth/enamel might exist among toothless and enamel-less lineages during evolution. Our study further considered that ACPT is a novel gene for studying tooth evolution.
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Affiliation(s)
- Yuan Mu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Xin Huang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Rui Liu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Yulin Gai
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Na Liang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Daiqing Yin
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Lei Shan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
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7
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Wang SK, Zhang H, Chavez MB, Hu Y, Seymen F, Koruyucu M, Kasimoglu Y, Colvin CD, Kolli TN, Tan MH, Wang YL, Lu PY, Kim JW, Foster BL, Bartlett JD, Simmer JP, Hu JCC. Dental malformations associated with biallelic MMP20 mutations. Mol Genet Genomic Med 2020; 8:e1307. [PMID: 32495503 PMCID: PMC7434610 DOI: 10.1002/mgg3.1307] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 12/30/2022] Open
Abstract
Background Matrix metallopeptidase 20 (MMP20) is an evolutionarily conserved protease that is essential for processing enamel matrix proteins during dental enamel formation. MMP20 mutations cause human autosomal recessive pigmented hypomaturation‐type amelogenesis imperfecta (AI2A2; OMIM #612529). MMP20 is expressed in both odontoblasts and ameloblasts, but its function during dentinogenesis is unclear. Methods We characterized 10 AI kindreds with MMP20 defects, characterized human third molars and/or Mmp20−/− mice by histology, Backscattered Scanning Electron Microscopy (bSEM), µCT, and nanohardness testing. Results We identified six novel MMP20 disease‐causing mutations. Four pathogenic variants were associated with exons encoding the MMP20 hemopexin‐like (PEX) domain, suggesting a necessary regulatory function. Mutant human enamel hardness was softest (13% of normal) midway between the dentinoenamel junction (DEJ) and the enamel surface. bSEM and µCT analyses of the third molars revealed reduced mineral density in both enamel and dentin. Dentin close to the DEJ showed an average hardness number 62%–69% of control. Characterization of Mmp20−/− mouse dentin revealed a significant reduction in dentin thickness and mineral density and a transient increase in predentin thickness, indicating disturbances in dentin matrix secretion and mineralization. Conclusion These results expand the spectrum of MMP20 disease‐causing mutations and provide the first evidence for MMP20 function during dentin formation.
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Affiliation(s)
- Shih-Kai Wang
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, Ann Arbor, MI, USA.,Department of Pediatric Dentistry, National Taiwan University School of Dentistry, Taipei City, Taiwan R.O.C
| | - Hong Zhang
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, Ann Arbor, MI, USA
| | - Michael B Chavez
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - Yuanyuan Hu
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, Ann Arbor, MI, USA
| | - Figen Seymen
- Department of Pedodontics, Istanbul University Faculty of Dentistry, Istanbul, Turkey
| | - Mine Koruyucu
- Department of Pedodontics, Istanbul University Faculty of Dentistry, Istanbul, Turkey
| | - Yelda Kasimoglu
- Department of Pedodontics, Istanbul University Faculty of Dentistry, Istanbul, Turkey
| | - Connor D Colvin
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - Tamara N Kolli
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - Michelle H Tan
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - Yin-Lin Wang
- Department of Pediatric Dentistry, National Taiwan University School of Dentistry, Taipei City, Taiwan R.O.C
| | - Pei-Ying Lu
- Department of Pediatric Dentistry, National Taiwan University School of Dentistry, Taipei City, Taiwan R.O.C
| | - Jung-Wook Kim
- Department of Pediatric Dentistry & Dental Research Institute, School of Dentistry, Seoul National University, Seoul, Republic of Korea.,Department of Molecular Genetics & Dental Research Institute, School of Dentistry, Seoul National University, Seoul, Republic of Korea
| | - Brian L Foster
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - John D Bartlett
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - James P Simmer
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, Ann Arbor, MI, USA
| | - Jan C-C Hu
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, Ann Arbor, MI, USA
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8
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Kim Y, Kang J, Seymen F, Koruyucu M, Zhang H, Kasimoglu Y, Bayram M, Tuna-Ince E, Bayrak S, Tuloglu N, Hu JC, Simmer J, Kim JW. Alteration of Exon Definition Causes Amelogenesis Imperfecta. J Dent Res 2020; 99:410-418. [PMID: 31999931 PMCID: PMC7088207 DOI: 10.1177/0022034520901708] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Amelogenesis imperfecta (AI) is a collection of genetic disorders affecting the quality and/or quantity of tooth enamel. More than 20 genes are, so far, known to be responsible for this condition. In this study, we recruited 3 Turkish families with hypomaturation AI. Whole-exome sequence analyses identified disease-causing mutations in each proband, and these mutations cosegregated with the AI phenotype in all recruited members of each family. The AI-causing mutations in family 1 were a novel AMELX mutation [NM_182680.1:c.143T>C, p.(Leu48Ser)] in the proband and a novel homozygous MMP20 mutation [NM_004771.3:c.616G>A, p.(Asp206Asn)] in the mother of the proband. Previously reported compound heterozygous MMP20 mutations [NM_004771.3:c.103A>C, p.(Arg35=) and c.389C>T, p.(Thr130Ile)] caused the AI in family 2 and family 3. Minigene splicing analyses revealed that the AMELX missense mutation increased exonic definition of exon 4 and the MMP20 synonymous mutation decreased exonic definition of exon 1. These mutations would trigger an alteration of exon usage during RNA splicing, causing the enamel malformations. These results broaden our understanding of molecular genetic pathology of tooth enamel formation.
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Affiliation(s)
- Y.J. Kim
- Department of Molecular Genetics & Dental Research Institute, School of Dentistry, Seoul National University, Seoul, Republic of Korea
| | - J. Kang
- Department of Pediatric Dentistry & Dental Research Institute, School of Dentistry, Seoul National University, Seoul, Republic of Korea
| | - F. Seymen
- Department of Pedodontics, Faculty of Dentistry, Istanbul University, Istanbul, Turkey
| | - M. Koruyucu
- Department of Pedodontics, Faculty of Dentistry, Istanbul University, Istanbul, Turkey
| | - H. Zhang
- Department of Biologic and Materials Sciences, School of Dentistry, University of Michigan, Ann Arbor, MI, USA
| | - Y. Kasimoglu
- Department of Pedodontics, Faculty of Dentistry, Istanbul University, Istanbul, Turkey
| | - M. Bayram
- Department of Pedodontics, Faculty of Dentistry, Istanbul Medipol University, Istanbul, Turkey
| | - E.B. Tuna-Ince
- Department of Pedodontics, Faculty of Dentistry, Istanbul University, Istanbul, Turkey
| | - S. Bayrak
- Department of Pediatric Dentistry, Faculty of Dentistry, University of Eskisehir Osmangazi, Eskisehir, Turkey
| | - N. Tuloglu
- Department of Pediatric Dentistry, Faculty of Dentistry, University of Eskisehir Osmangazi, Eskisehir, Turkey
| | - J.C.-C. Hu
- Department of Biologic and Materials Sciences, School of Dentistry, University of Michigan, Ann Arbor, MI, USA
| | - J.P. Simmer
- Department of Biologic and Materials Sciences, School of Dentistry, University of Michigan, Ann Arbor, MI, USA
| | - J.-W. Kim
- Department of Molecular Genetics & Dental Research Institute, School of Dentistry, Seoul National University, Seoul, Republic of Korea
- Department of Pediatric Dentistry & Dental Research Institute, School of Dentistry, Seoul National University, Seoul, Republic of Korea
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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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Sharma V, Hiller M. Losses of human disease-associated genes in placental mammals. NAR Genom Bioinform 2019; 2:lqz012. [PMID: 33575564 PMCID: PMC7671337 DOI: 10.1093/nargab/lqz012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/24/2019] [Accepted: 10/08/2019] [Indexed: 02/07/2023] Open
Abstract
We systematically investigate whether losses of human disease-associated genes occurred in other mammals during evolution. We first show that genes lost in any of 62 non-human mammals generally have a lower degree of pleiotropy, and are highly depleted in essential and disease-associated genes. Despite this under-representation, we discovered multiple genes implicated in human disease that are truly lost in non-human mammals. In most cases, traits resembling human disease symptoms are present but not deleterious in gene-loss species, exemplified by losses of genes causing human eye or teeth disorders in poor-vision or enamel-less mammals. We also found widespread losses of PCSK9 and CETP genes, where loss-of-function mutations in humans protect from atherosclerosis. Unexpectedly, we discovered losses of disease genes (TYMP, TBX22, ABCG5, ABCG8, MEFV, CTSE) where deleterious phenotypes do not manifest in the respective species. A remarkable example is the uric acid-degrading enzyme UOX, which we found to be inactivated in elephants and manatees. While UOX loss in hominoids led to high serum uric acid levels and a predisposition for gout, elephants and manatees exhibit low uric acid levels, suggesting alternative ways of metabolizing uric acid. Together, our results highlight numerous mammals that are 'natural knockouts' of human disease genes.
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Affiliation(s)
- Virag Sharma
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany.,Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany.,Center for Systems Biology Dresden, 01307 Dresden, Germany
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11
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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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12
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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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Lammers M, Kraaijeveld K, Mariën J, Ellers J. Gene expression changes associated with the evolutionary loss of a metabolic trait: lack of lipogenesis in parasitoids. BMC Genomics 2019; 20:309. [PMID: 31014246 PMCID: PMC6480896 DOI: 10.1186/s12864-019-5673-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 04/08/2019] [Indexed: 12/24/2022] Open
Abstract
Background Trait loss is a pervasive phenomenon in evolution, yet the underlying molecular causes have been identified in only a handful of cases. Most of these cases involve loss-of-function mutations in one or more trait-specific genes. However, in parasitoid insects the evolutionary loss of a metabolic trait is not associated with gene decay. Parasitoids have lost the ability to convert dietary sugars into fatty acids. Earlier research suggests that lack of lipogenesis in the parasitoid wasp Nasonia vitripennis is caused by changes in gene regulation. Results We compared transcriptomic responses to sugar-feeding in the non-lipogenic parasitoid species Nasonia vitripennis and the lipogenic Drosophila melanogaster. Both species adjusted their metabolism within 4 hours after sugar-feeding, but there were sharp differences between the expression profiles of the two species, especially in the carbohydrate and lipid metabolic pathways. Several genes coding for key enzymes in acetyl-CoA metabolism, such as malonyl-CoA decarboxylase (mcd) and HMG-CoA synthase (hmgs) differed in expression between the two species. Their combined action likely blocks lipogenesis in the parasitoid species. Network-based analysis showed connectivity of genes to be negatively correlated to the fold change of gene expression. Furthermore, genes involved in the fatty acid metabolic pathway were more connected than the set of genes of all metabolic pathways combined. Conclusion High connectivity of lipogenesis genes is indicative of pleiotropic effects and could explain the absence of gene degradation. We conclude that modification of expression levels of only a few little-connected genes, such as mcd, is sufficient to enable complete loss of lipogenesis in N. vitripennis. Electronic supplementary material The online version of this article (10.1186/s12864-019-5673-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mark Lammers
- Department of Ecological Sciences, Section Animal Ecology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.
| | - Ken Kraaijeveld
- Department of Ecological Sciences, Section Animal Ecology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Janine Mariën
- Department of Ecological Sciences, Section Animal Ecology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Jacintha Ellers
- Department of Ecological Sciences, Section Animal Ecology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
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14
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Kim J, Zhang H, Seymen F, Koruyucu M, Hu Y, Kang J, Kim YJ, Ikeda A, Kasimoglu Y, Bayram M, Zhang C, Kawasaki K, Bartlett JD, Saunders TL, Simmer JP, Hu JC. Mutations in RELT cause autosomal recessive amelogenesis imperfecta. Clin Genet 2019; 95:375-383. [PMID: 30506946 PMCID: PMC6392136 DOI: 10.1111/cge.13487] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 12/16/2022]
Abstract
Amelogenesis imperfecta (AI) is a collection of isolated (non-syndromic) inherited diseases affecting dental enamel formation or a clinical phenotype in syndromic conditions. We characterized three consanguineous AI families with generalized irregular hypoplastic enamel with rapid attrition that perfectly segregated with homozygous defects in a novel gene: RELT that is a member of the tumor necrosis factor receptor superfamily (TNFRSF). RNAscope in situ hybridization of wild-type mouse molars and incisors showed specific Relt mRNA expression by secretory stage ameloblasts and by odontoblasts. Relt-/- mice generated by CRISPR/Cas9 exhibited incisor and molar enamel malformations. Relt-/- enamel had a rough surface and underwent rapid attrition. Normally unmineralized spaces in the deep enamel near the dentino-enamel junction (DEJ) were as highly mineralized as the adjacent enamel, which likely altered the mechanical properties of the DEJ. Phylogenetic analyses showed the existence of selective pressure on RELT gene outside of tooth development, indicating that the human condition may be syndromic, which possibly explains the history of small stature and severe childhood infections in two of the probands. Knowing a TNFRSF member is critical during the secretory stage of enamel formation advances our understanding of amelogenesis and improves our ability to diagnose human conditions featuring enamel malformations.
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Affiliation(s)
- Jung‐Wook Kim
- Department of Pediatric Dentistry & Dental Research Institute, School of DentistrySeoul National UniversitySeoulRepublic of Korea
- Department of Molecular Genetics & the Dental Research Institute, School of DentistrySeoul National UniversitySeoulRepublic of Korea
| | - Hong Zhang
- Department of Biologic and Materials SciencesUniversity of Michigan School of DentistryAnn ArborMichigan
| | - Figen Seymen
- Department of Pedodontics, Faculty of DentistryIstanbul UniversityIstanbulTurkey
| | - Mine Koruyucu
- Department of Pedodontics, Faculty of DentistryIstanbul UniversityIstanbulTurkey
| | - Yuanyuan Hu
- Department of Biologic and Materials SciencesUniversity of Michigan School of DentistryAnn ArborMichigan
| | - Jenny Kang
- Department of Pediatric Dentistry & Dental Research Institute, School of DentistrySeoul National UniversitySeoulRepublic of Korea
| | - Youn J. Kim
- Department of Molecular Genetics & the Dental Research Institute, School of DentistrySeoul National UniversitySeoulRepublic of Korea
| | - Atsushi Ikeda
- Division of BiosciencesThe Ohio State University, College of DentistryColumbusOhio
| | - Yelda Kasimoglu
- Department of Pedodontics, Faculty of DentistryIstanbul UniversityIstanbulTurkey
| | - Merve Bayram
- Department of Pedodontics, Faculty of DentistryIstanbul Medipol UniversityIstanbulTurkey
| | - Chuhua Zhang
- Department of Biologic and Materials SciencesUniversity of Michigan School of DentistryAnn ArborMichigan
| | - Kazuhiko Kawasaki
- Department of AnthropologyPenn State UniversityUniversity ParkPennsylvania
| | - John D. Bartlett
- Division of BiosciencesThe Ohio State University, College of DentistryColumbusOhio
| | - Thomas L. Saunders
- Department of Internal Medicine, Division of Molecular, Medicine and GeneticsUniversity of Michigan Medical SchoolAnn ArborMichigan
| | - 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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15
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Springer MS, Emerling CA, Gatesy J, Randall J, Collin MA, Hecker N, Hiller M, Delsuc F. Odontogenic ameloblast-associated (ODAM) is inactivated in toothless/enamelless placental mammals and toothed whales. BMC Evol Biol 2019; 19:31. [PMID: 30674270 PMCID: PMC6343362 DOI: 10.1186/s12862-019-1359-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 01/11/2019] [Indexed: 11/10/2022] Open
Abstract
Background The gene for odontogenic ameloblast-associated (ODAM) is a member of the secretory calcium-binding phosphoprotein gene family. ODAM is primarily expressed in dental tissues including the enamel organ and the junctional epithelium, and may also have pleiotropic functions that are unrelated to teeth. Here, we leverage the power of natural selection to test competing hypotheses that ODAM is tooth-specific versus pleiotropic. Specifically, we compiled and screened complete protein-coding sequences, plus sequences for flanking intronic regions, for ODAM in 165 placental mammals to determine if this gene contains inactivating mutations in lineages that either lack teeth (baleen whales, pangolins, anteaters) or lack enamel on their teeth (aardvarks, sloths, armadillos), as would be expected if the only essential functions of ODAM are related to tooth development and the adhesion of the gingival junctional epithelium to the enamel tooth surface. Results We discovered inactivating mutations in all species of placental mammals that either lack teeth or lack enamel on their teeth. A surprising result is that ODAM is also inactivated in a few additional lineages including all toothed whales that were examined. We hypothesize that ODAM inactivation is related to the simplified outer enamel surface of toothed whales. An alternate hypothesis is that ODAM inactivation in toothed whales may be related to altered antimicrobial functions of the junctional epithelium in aquatic habitats. Selection analyses on ODAM sequences revealed that the composite dN/dS value for pseudogenic branches is close to 1.0 as expected for a neutrally evolving pseudogene. DN/dS values on transitional branches were used to estimate ODAM inactivation times. In the case of pangolins, ODAM was inactivated ~ 65 million years ago, which is older than the oldest pangolin fossil (Eomanis, 47 Ma) and suggests an even more ancient loss or simplification of teeth in this lineage. Conclusion Our results validate the hypothesis that the only essential functions of ODAM that are maintained by natural selection are related to tooth development and/or the maintenance of a healthy junctional epithelium that attaches to the enamel surface of teeth. Electronic supplementary material The online version of this article (10.1186/s12862-019-1359-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mark S Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92521, USA.
| | - Christopher A Emerling
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France.,Department of Biology, Whittier College, Whittier, CA, 90602, USA
| | - John Gatesy
- Division of Vertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA
| | - Jason Randall
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Matthew A Collin
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Nikolai Hecker
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| | - Frédéric Delsuc
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
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16
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Lanzetti A, Berta A, Ekdale EG. Prenatal Development of the Humpback Whale: Growth Rate, Tooth Loss and Skull Shape Changes in an Evolutionary Framework. Anat Rec (Hoboken) 2018; 303:180-204. [DOI: 10.1002/ar.23990] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 01/15/2018] [Accepted: 01/24/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Agnese Lanzetti
- Department of BiologySan Diego State University San Diego California
| | - Annalisa Berta
- Department of BiologySan Diego State University San Diego California
| | - Eric G. Ekdale
- Department of BiologySan Diego State University San Diego California
- San Diego Natural History Museum San Diego California
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17
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Tsai CH, Fordyce RE. A new archaic baleen whale Toipahautea waitaki (early Late Oligocene, New Zealand) and the origins of crown Mysticeti. ROYAL SOCIETY OPEN SCIENCE 2018; 5:172453. [PMID: 29765689 PMCID: PMC5936954 DOI: 10.1098/rsos.172453] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 03/13/2018] [Indexed: 06/08/2023]
Abstract
A new genus and species of extinct baleen whale †Toipahautea waitaki (Late Oligocene, New Zealand) is based on a skull and associated bones, from the lower Kokoamu Greensand, about 27.5 Ma (local upper Whaingaroan Stage, early Chattian). The upper jaw includes a thin, elongate and apparently toothless maxilla, with evidence of arterial supply for baleen. Open sutures with the premaxilla suggest a flexible (kinetic) upper jaw. The blowhole is well forward. The mandible is bowed laterally and slightly dorsally; unlike the Eomysticetidae, there are no mandibular alveoli, and the coronoid process is tapered and curved laterally. Jaw structure is consistent with baleen-assisted gulp-feeding. The age of early Chattian makes †Toipahautea a very early, if not the oldest named, toothless and baleen-bearing mysticete, suggesting that the full transition from toothed to baleen-bearing probably occurred in the Early Oligocene. Late Oligocene mysticetes vary considerably in jaw form and kinesis, tooth form and function, and development of baleen, implying a wide range of raptorial, suctorial and filter-feeding behaviour. More study may elucidate the function of jaws, teeth and baleen in terms of opportunist/generalist feeding, as in modern gray whales, versus specialized feeding. We here propose that early mysticetes, when transitioned from toothed to baleen-bearing, were generalists and opportunists instead of specializing in any forms of feeding strategies. In addition, two different phylogenetic analyses placed †Toipahautea either in a polytomy including crown Mysticeti, or immediately basal to the crown, and above †Eomysticetidae in both cases. Because the †Toipahautea waitaki holotype is an immature individual, it may plot more basally in phylogeny than its true position.
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Affiliation(s)
- Cheng-Hsiu Tsai
- Department of Geology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Department of Geology and Paleontology, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba 305-0005, Japan
| | - R. Ewan Fordyce
- Department of Geology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7013, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7013, USA
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18
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Emerling CA, Widjaja AD, Nguyen NN, Springer MS. Their loss is our gain: regressive evolution in vertebrates provides genomic models for uncovering human disease loci. J Med Genet 2017; 54:787-794. [PMID: 28814606 DOI: 10.1136/jmedgenet-2017-104837] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/07/2017] [Accepted: 07/10/2017] [Indexed: 12/20/2022]
Abstract
Throughout Earth's history, evolution's numerous natural 'experiments' have resulted in a diverse range of phenotypes. Though de novo phenotypes receive widespread attention, degeneration of traits inherited from an ancestor is a very common, yet frequently neglected, evolutionary path. The latter phenomenon, known as regressive evolution, often results in vertebrates with phenotypes that mimic inherited disease states in humans. Regressive evolution of anatomical and/or physiological traits is typically accompanied by inactivating mutations underlying these traits, which frequently occur at loci identical to those implicated in human diseases. Here we discuss the potential utility of examining the genomes of vertebrates that have experienced regressive evolution to inform human medical genetics. This approach is low cost and high throughput, giving it the potential to rapidly improve knowledge of disease genetics. We discuss two well-described examples, rod monochromacy (congenital achromatopsia) and amelogenesis imperfecta, to demonstrate the utility of this approach, and then suggest methods to equip non-experts with the ability to corroborate candidate genes and uncover new disease loci.
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Affiliation(s)
- Christopher A Emerling
- Museum of Vertebrate Zoology, University of California, Berkeley, California, USA
- Department of Biology, University of California, Riverside, California, USA
| | - Andrew D Widjaja
- Department of Biochemistry, University of California, Riverside, California, USA
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California, USA
| | - Nancy N Nguyen
- Department of Bioengineering, University of California, Riverside, California, USA
- Department of Bioengineering, University of California, Los Angeles, California, USA
| | - Mark S Springer
- Department of Biology, University of California, Riverside, California, USA
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19
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Kishida T, Suzuki M, Takayama A. Evolution of the alternative AQP2 gene: Acquisition of a novel protein-coding sequence in dolphins. Mol Phylogenet Evol 2017; 118:54-57. [PMID: 28943376 DOI: 10.1016/j.ympev.2017.09.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 08/23/2017] [Accepted: 09/18/2017] [Indexed: 12/01/2022]
Abstract
Taxon-specific de novo protein-coding sequences are thought to be important for taxon-specific environmental adaptation. A recent study revealed that bottlenose dolphins acquired a novel isoform of aquaporin 2 generated by alternative splicing (alternative AQP2), which helps dolphins to live in hyperosmotic seawater. The AQP2 gene consists of four exons, but the alternative AQP2 gene lacks the fourth exon and instead has a longer third exon that includes the original third exon and a part of the original third intron. Here, we show that the latter half of the third exon of the alternative AQP2 arose from a non-protein-coding sequence. Intact ORF of this de novo sequence is shared not by all cetaceans, but only by delphinoids. However, this sequence is conservative in all modern cetaceans, implying that this de novo sequence potentially plays important roles for marine adaptation in cetaceans.
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Affiliation(s)
- Takushi Kishida
- Wildlife Research Center, Kyoto University, 2-24 Tanaka Sekiden-cho, Sakyo, Kyoto 606-8203, Japan.
| | - Miwa Suzuki
- Department of Marine Science and Resources, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan.
| | - Asuka Takayama
- Department of Marine Science and Resources, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan
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20
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Gaudry MJ, Campbell KL. Evolution of UCP1 Transcriptional Regulatory Elements Across the Mammalian Phylogeny. Front Physiol 2017; 8:670. [PMID: 28979209 PMCID: PMC5611445 DOI: 10.3389/fphys.2017.00670] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 08/23/2017] [Indexed: 01/22/2023] Open
Abstract
Uncoupling protein 1 (UCP1) permits non-shivering thermogenesis (NST) when highly expressed in brown adipose tissue (BAT) mitochondria. Exclusive to placental mammals, BAT has commonly been regarded to be advantageous for thermoregulation in hibernators, small-bodied species, and the neonates of larger species. While numerous regulatory control motifs associated with UCP1 transcription have been proposed for murid rodents, it remains unclear whether these are conserved across the eutherian mammal phylogeny and hence essential for UCP1 expression. To address this shortcoming, we conducted a broad comparative survey of putative UCP1 transcriptional regulatory elements in 139 mammals (135 eutherians). We find no evidence for presence of a UCP1 enhancer in monotremes and marsupials, supporting the hypothesis that this control region evolved in a stem eutherian ancestor. We additionally reveal that several putative promoter elements (e.g., CRE-4, CCAAT) identified in murid rodents are not conserved among BAT-expressing eutherians, and together with the putative regulatory region (PRR) and CpG island do not appear to be crucial for UCP1 expression. The specificity and importance of the upTRE, dnTRE, URE1, CRE-2, RARE-2, NBRE, BRE-1, and BRE-2 enhancer elements first described from rats and mice are moreover uncertain as these motifs differ substantially—but generally remain highly conserved—in other BAT-expressing eutherians. Other UCP1 enhancer motifs (CRE-3, PPRE, and RARE-3) as well as the TATA box are also highly conserved in nearly all eutherian lineages with an intact UCP1. While these transcriptional regulatory motifs are generally also maintained in species where this gene is pseudogenized, the loss or degeneration of key basal promoter (e.g., TATA box) and enhancer elements in other UCP1-lacking lineages make it unlikely that the enhancer region is pleiotropic (i.e., co-regulates additional genes). Importantly, differential losses of (or mutations within) putative regulatory elements among the eutherian lineages with an intact UCP1 suggests that the transcriptional control of gene expression is not highly conserved in this mammalian clade.
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Affiliation(s)
- Michael J Gaudry
- Department of Biological Sciences, University of ManitobaWinnipeg, MB, Canada
| | - Kevin L Campbell
- Department of Biological Sciences, University of ManitobaWinnipeg, MB, Canada
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Gasse B, Prasad M, Delgado S, Huckert M, Kawczynski M, Garret-Bernardin A, Lopez-Cazaux S, Bailleul-Forestier I, Manière MC, Stoetzel C, Bloch-Zupan A, Sire JY. Evolutionary Analysis Predicts Sensitive Positions of MMP20 and Validates Newly- and Previously-Identified MMP20 Mutations Causing Amelogenesis Imperfecta. Front Physiol 2017; 8:398. [PMID: 28659819 PMCID: PMC5469888 DOI: 10.3389/fphys.2017.00398] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/26/2017] [Indexed: 12/21/2022] Open
Abstract
Amelogenesis imperfecta (AI) designates a group of genetic diseases characterized by a large range of enamel disorders causing important social and health problems. These defects can result from mutations in enamel matrix proteins or protease encoding genes. A range of mutations in the enamel cleavage enzyme matrix metalloproteinase-20 gene (MMP20) produce enamel defects of varying severity. To address how various alterations produce a range of AI phenotypes, we performed a targeted analysis to find MMP20 mutations in French patients diagnosed with non-syndromic AI. Genomic DNA was isolated from saliva and MMP20 exons and exon-intron boundaries sequenced. We identified several homozygous or heterozygous mutations, putatively involved in the AI phenotypes. To validate missense mutations and predict sensitive positions in the MMP20 sequence, we evolutionarily compared 75 sequences extracted from the public databases using the Datamonkey webserver. These sequences were representative of mammalian lineages, covering more than 150 million years of evolution. This analysis allowed us to find 324 sensitive positions (out of the 483 MMP20 residues), pinpoint functionally important domains, and build an evolutionary chart of important conserved MMP20 regions. This is an efficient tool to identify new- and previously-identified mutations. We thus identified six functional MMP20 mutations in unrelated families, finding two novel mutated sites. The genotypes and phenotypes of these six mutations are described and compared. To date, 13 MMP20 mutations causing AI have been reported, making these genotypes and associated hypomature enamel phenotypes the most frequent in AI.
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Affiliation(s)
- Barbara Gasse
- Institut de Biologie Paris-Seine, UMR 7138-Evolution Paris-Seine, Sorbonne Universités, Université Pierre et Marie CurieParis, France
| | - Megana Prasad
- Laboratoire de Génétique Médicale, Institut National de la Santé et de la Recherche Médicale UMRS_1112, Institut de Génétique Médicale d'Alsace, FMTS, Université de StrasbourgStrasbourg, France
| | - Sidney Delgado
- Institut de Biologie Paris-Seine, UMR 7138-Evolution Paris-Seine, Sorbonne Universités, Université Pierre et Marie CurieParis, France
| | - Mathilde Huckert
- Laboratoire de Génétique Médicale, Institut National de la Santé et de la Recherche Médicale UMRS_1112, Institut de Génétique Médicale d'Alsace, FMTS, Université de StrasbourgStrasbourg, France.,Faculté de Chirurgie Dentaire, Université de StrasbourgStrasbourg, France
| | - Marzena Kawczynski
- Faculté de Chirurgie Dentaire, Université de StrasbourgStrasbourg, France.,Pôle de Médecine et Chirurgie Bucco-Dentaires, Centre de Référence des Manifestations Odontologiques des Maladies Rares, O-Rares, Hôpitaux Universitaires de StrasbourgStrasbourg, France
| | - Annelyse Garret-Bernardin
- Faculté de Chirurgie Dentaire, Université de StrasbourgStrasbourg, France.,Unit of Dentistry, IRCCS, Bambino Gesù Children's HospitalRome, Italy
| | - Serena Lopez-Cazaux
- Faculté de Chirurgie Dentaire, Département d'Odontologie Pédiatrique, Centre de Compétences Maladies Rares, CHU Hôtel Dieu, Service d'odontologie Conservatrice et PédiatriqueNantes, France
| | - Isabelle Bailleul-Forestier
- Faculté de Chirurgie Dentaire, CHU de Toulouse, Centre de Compétences Maladies Rares, Odontologie Pédiatrique, Université Paul SabatierToulouse, France
| | - Marie-Cécile Manière
- Faculté de Chirurgie Dentaire, Université de StrasbourgStrasbourg, France.,Pôle de Médecine et Chirurgie Bucco-Dentaires, Centre de Référence des Manifestations Odontologiques des Maladies Rares, O-Rares, Hôpitaux Universitaires de StrasbourgStrasbourg, France
| | - Corinne Stoetzel
- Laboratoire de Génétique Médicale, Institut National de la Santé et de la Recherche Médicale UMRS_1112, Institut de Génétique Médicale d'Alsace, FMTS, Université de StrasbourgStrasbourg, France
| | - Agnès Bloch-Zupan
- Faculté de Chirurgie Dentaire, Université de StrasbourgStrasbourg, France.,Pôle de Médecine et Chirurgie Bucco-Dentaires, Centre de Référence des Manifestations Odontologiques des Maladies Rares, O-Rares, Hôpitaux Universitaires de StrasbourgStrasbourg, France.,Centre Européen de Recherche en Biologie et en Médecine, Centre National de la Recherche Scientifique UMR7104, Institut National de la Santé et de la Recherche Médicale U964, Institut de Génétique et de Biologie Moléculaire and Cellulaire, Université de StrasbourgIllkirch, France.,Institut d'Etudes Avancées, Université de Strasbourg, USIASStrasbourg, France.,Eastman Dental Institute, University College LondonLondon, United Kingdom
| | - Jean-Yves Sire
- Institut de Biologie Paris-Seine, UMR 7138-Evolution Paris-Seine, Sorbonne Universités, Université Pierre et Marie CurieParis, France
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22
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Suzuki TK. On the Origin of Complex Adaptive Traits: Progress Since the Darwin Versus Mivart Debate. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2017; 328:304-320. [PMID: 28397400 DOI: 10.1002/jez.b.22740] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 03/02/2017] [Accepted: 03/07/2017] [Indexed: 01/12/2023]
Abstract
The evolutionary origin of complex adaptive traits has been a controversial topic in the history of evolutionary biology. Although Darwin argued for the gradual origins of complex adaptive traits within the theory of natural selection, Mivart insisted that natural selection could not account for the incipient stages of complex traits. The debate starting from Darwin and Mivart eventually engendered two opposite views: gradualism and saltationism. Although this has been a long-standing debate, the issue remains unresolved. However, recent studies have interrogated classic examples of complex traits, such as the asymmetrical eyes of flatfishes and leaf mimicry of butterfly wings, whose origins were debated by Darwin and Mivart. Here, I review recent findings as a starting point to provide a modern picture of the evolution of complex adaptive traits. First, I summarize the empirical evidence that unveils the evolutionary steps toward complex traits. I then argue that the evolution of complex traits could be understood within the concept of "reducible complexity." Through these discussions, I propose a conceptual framework for the formation of complex traits, named as reducible-composable multicomponent systems, that satisfy two major characteristics: reducibility into a sum of subcomponents and composability to construct traits from various additional and combinatorial arrangements of the subcomponents. This conceptual framework provides an analytical foundation for exploring evolutionary pathways to build up complex traits. This review provides certain essential avenues for deciphering the origin of complex adaptive traits.
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Affiliation(s)
- Takao K Suzuki
- Transgenic Silkworm Research Unit, Division of Biotechnology, Institute of Agrobiological Sciences, NARO, Ibaraki, 305-8634, Japan
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23
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Springer MS, Gatesy J. Inactivation of the olfactory marker protein (OMP) gene in river dolphins and other odontocete cetaceans. Mol Phylogenet Evol 2017; 109:375-387. [PMID: 28193458 DOI: 10.1016/j.ympev.2017.01.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 01/25/2017] [Accepted: 01/29/2017] [Indexed: 11/18/2022]
Abstract
Various toothed whales (Odontoceti) are unique among mammals in lacking olfactory bulbs as adults and are thought to be anosmic (lacking the olfactory sense). At the molecular level, toothed whales have high percentages of pseudogenic olfactory receptor genes, but species that have been investigated to date retain an intact copy of the olfactory marker protein gene (OMP), which is highly expressed in olfactory receptor neurons and may regulate the temporal resolution of olfactory responses. One hypothesis for the retention of intact OMP in diverse odontocete lineages is that this gene is pleiotropic with additional functions that are unrelated to olfaction. Recent expression studies provide some support for this hypothesis. Here, we report OMP sequences for representatives of all extant cetacean families and provide the first molecular evidence for inactivation of this gene in vertebrates. Specifically, OMP exhibits independent inactivating mutations in six different odontocete lineages: four river dolphin genera (Platanista, Lipotes, Pontoporia, Inia), sperm whale (Physeter), and harbor porpoise (Phocoena). These results suggest that the only essential role of OMP that is maintained by natural selection is in olfaction, although a non-olfactory role for OMP cannot be ruled out for lineages that retain an intact copy of this gene. Available genome sequences from cetaceans and close outgroups provide evidence of inactivating mutations in two additional genes (CNGA2, CNGA4), which imply further pseudogenization events in the olfactory cascade of odontocetes. Selection analyses demonstrate that evolutionary constraints on all three genes (OMP, CNGA2, CNGA4) have been greatly reduced in Odontoceti, but retain a signature of purifying selection on the stem Cetacea branch and in Mysticeti (baleen whales). This pattern is compatible with the 'echolocation-priority' hypothesis for the evolution of OMP, which posits that negative selection was maintained in the common ancestor of Cetacea and was not relaxed significantly until the evolution of echolocation in Odontoceti.
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Affiliation(s)
- Mark S Springer
- Department of Biology, University of California, Riverside, CA 92521, USA.
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA.
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24
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Berta A, Lanzetti A, Ekdale EG, Deméré TA. From Teeth to Baleen and Raptorial to Bulk Filter Feeding in Mysticete Cetaceans: The Role of Paleontological, Genetic, and Geochemical Data in Feeding Evolution and Ecology. Integr Comp Biol 2016; 56:1271-1284. [DOI: 10.1093/icb/icw128] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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25
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Prudent X, Parra G, Schwede P, Roscito JG, Hiller M. Controlling for Phylogenetic Relatedness and Evolutionary Rates Improves the Discovery of Associations Between Species' Phenotypic and Genomic Differences. Mol Biol Evol 2016; 33:2135-50. [PMID: 27222536 PMCID: PMC4948712 DOI: 10.1093/molbev/msw098] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The growing number of sequenced genomes allows us now to address a key question in genetics and evolutionary biology: which genomic changes underlie particular phenotypic changes between species? Previously, we developed a computational framework called Forward Genomics that associates phenotypic to genomic differences by focusing on phenotypes that are independently lost in different lineages. However, our previous implementation had three main limitations. Here, we present two new Forward Genomics methods that overcome these limitations by (1) directly controlling for phylogenetic relatedness, (2) controlling for differences in evolutionary rates, and (3) computing a statistical significance. We demonstrate on large-scale simulated data and on real data that both new methods substantially improve the sensitivity to detect associations between phenotypic and genomic differences. We applied these new methods to detect genomic differences involved in the loss of vision in the blind mole rat and the cape golden mole, two independent subterranean mammals. Forward Genomics identified several genes that are enriched in functions related to eye development and the perception of light, as well as genes involved in the circadian rhythm. These new Forward Genomics methods represent a significant advance in our ability to discover the genomic basis underlying phenotypic differences between species. Source code: https://github.com/hillerlab/ForwardGenomics/.
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Affiliation(s)
- Xavier Prudent
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Genis Parra
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Peter Schwede
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Juliana G Roscito
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
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26
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Murine matrix metalloproteinase-20 overexpression stimulates cell invasion into the enamel layer via enhanced Wnt signaling. Sci Rep 2016; 6:29492. [PMID: 27403713 PMCID: PMC4941722 DOI: 10.1038/srep29492] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 06/17/2016] [Indexed: 12/18/2022] Open
Abstract
Matrix metalloproteinase-20 (MMP20) is expressed by ameloblasts in developing teeth and MMP20 mutations cause enamel malformation. We established a stably transfected Tet-Off Mmp20-inducible ameloblast-lineage cell line and found that MMP20 expression promoted cell invasion. Previously, we engineered transgenic mice (Tg) that drive Mmp20 expression and showed that Mmp20(+/+)Tg mice had soft enamel. Here we asked if Mmp20 overexpression disrupts ameloblast function. Incisors from Mmp20(+/+) mice expressing the Mmp20 Tg had a striking cell infiltrate which nearly replaced the entire enamel layer. A thin layer of enamel-like material remained over the dentin and at the outer tooth surface, but between these regions were invading fibroblasts and epithelial cells that surrounded ectopic bone-like calcifications. Mmp20(+/+)Tg mice had decreased enamel organ cadherin levels compared to the Mmp20 ablated and WT mice and, instead of predominantly locating adjacent to the ameloblast cell membrane, β-catenin was predominantly present within the nuclei of invading cells. Our data suggest that increased cadherin cleavage by transgenic MMP20 in the WT background releases excess β-catenin, which translocates to ameloblast nuclei to promote cell migration/invasion. Therefore, we conclude that MMP20 plays a role in normal ameloblast migration through tightly controlled Wnt signaling and that MMP20 overexpression disrupts this process.
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27
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Elucidating the evolution of hominid dentition in the age of phenomics, modularity, and quantitative genetics. Ann Anat 2016; 203:3-11. [DOI: 10.1016/j.aanat.2015.05.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 05/17/2015] [Accepted: 05/18/2015] [Indexed: 12/11/2022]
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28
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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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29
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Inactivation of C4orf26 in toothless placental mammals. Mol Phylogenet Evol 2015; 95:34-45. [PMID: 26596502 DOI: 10.1016/j.ympev.2015.11.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 10/22/2015] [Accepted: 11/03/2015] [Indexed: 01/11/2023]
Abstract
Previous studies have reported inactivated copies of six enamel-related genes (AMBN, AMEL, AMTN, ENAM, KLK4, MMP20) and one dentin-related gene (DSPP) in one or more toothless vertebrates and/or vertebrates with enamelless teeth, thereby providing evidence that these genes are enamel or tooth-specific with respect to their critical functions that are maintained by natural selection. Here, we employ available genome sequences for edentulous and enamelless mammals to evaluate the enamel specificity of four genes (WDR72, SLC24A4, FAM83H, C4orf26) that have been implicated in amelogenesis imperfecta, a condition in which proper enamel formation is abrogated during tooth development. Coding sequences for WDR72, SCL24A4, and FAM83H are intact in four edentulous taxa (Chinese pangolin, three baleen whales) and three taxa (aardvark, nine-banded armadillo, Hoffmann's two-toed sloth) with enamelless teeth, suggesting that these genes have critical functions beyond their involvement in tooth development. By contrast, genomic data for C4orf26 reveal inactivating mutations in pangolin and bowhead whale as well as evidence for deletion of this gene in two minke whale species. Hybridization capture of exonic regions and PCR screens provide evidence for inactivation of C4orf26 in eight additional baleen whale species. However, C4orf26 is intact in all three species with enamelless teeth that were surveyed, as well as in 95 additional mammalian species with enamel-capped teeth. Estimates of selection intensity suggest that dN/dS ratios on branches leading to taxa with enamelless teeth are similar to the dN/dS ratio on branches leading to taxa with enamel-capped teeth. Based on these results, we conclude that C4orf26 is tooth-specific, but not enamel-specific, with respect to its essential functions that are maintained by natural selection. A caveat is that an alternative splice site variant, which translates exon 3 in a different reading frame, is putatively functional in Catarrhini and may have evolved an additional role in this primate clade.
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30
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Boessenecker RW, Fordyce RE. A new genus and species of eomysticetid (Cetacea: Mysticeti) and a reinterpretation of ‘Mauicetus’lophocephalus Marples, 1956: Transitional baleen whales from the upper Oligocene of New Zealand. Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12297] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Robert W. Boessenecker
- Department of Geology; University of Otago; 360 Leith Walk, PO Box 56 9010 Dunedin New Zealand
- University of California Museum of Paleontology; 94720 Berkeley CA USA
| | - R. Ewan Fordyce
- Department of Geology; University of Otago; 360 Leith Walk, PO Box 56 9010 Dunedin New Zealand
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31
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Springer MS, Signore AV, Paijmans JLA, Vélez-Juarbe J, Domning DP, Bauer CE, He K, Crerar L, Campos PF, Murphy WJ, Meredith RW, Gatesy J, Willerslev E, MacPhee RDE, Hofreiter M, Campbell KL. Interordinal gene capture, the phylogenetic position of Steller's sea cow based on molecular and morphological data, and the macroevolutionary history of Sirenia. Mol Phylogenet Evol 2015; 91:178-93. [PMID: 26050523 DOI: 10.1016/j.ympev.2015.05.022] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 05/22/2015] [Accepted: 05/28/2015] [Indexed: 01/02/2023]
Abstract
The recently extinct (ca. 1768) Steller's sea cow (Hydrodamalis gigas) was a large, edentulous North Pacific sirenian. The phylogenetic affinities of this taxon to other members of this clade, living and extinct, are uncertain based on previous morphological and molecular studies. We employed hybridization capture methods and second generation sequencing technology to obtain >30kb of exon sequences from 26 nuclear genes for both H. gigas and Dugong dugon. We also obtained complete coding sequences for the tooth-related enamelin (ENAM) gene. Hybridization probes designed using dugong and manatee sequences were both highly effective in retrieving sequences from H. gigas (mean=98.8% coverage), as were more divergent probes for regions of ENAM (99.0% coverage) that were designed exclusively from a proboscidean (African elephant) and a hyracoid (Cape hyrax). New sequences were combined with available sequences for representatives of all other afrotherian orders. We also expanded a previously published morphological matrix for living and fossil Sirenia by adding both new taxa and nine new postcranial characters. Maximum likelihood and parsimony analyses of the molecular data provide robust support for an association of H. gigas and D. dugon to the exclusion of living trichechids (manatees). Parsimony analyses of the morphological data also support the inclusion of H. gigas in Dugongidae with D. dugon and fossil dugongids. Timetree analyses based on calibration density approaches with hard- and soft-bounded constraints suggest that H. gigas and D. dugon diverged in the Oligocene and that crown sirenians last shared a common ancestor in the Eocene. The coding sequence for the ENAM gene in H. gigas does not contain frameshift mutations or stop codons, but there is a transversion mutation (AG to CG) in the acceptor splice site of intron 2. This disruption in the edentulous Steller's sea cow is consistent with previous studies that have documented inactivating mutations in tooth-specific loci of a variety of edentulous and enamelless vertebrates including birds, turtles, aardvarks, pangolins, xenarthrans, and baleen whales. Further, branch-site dN/dS analyses provide evidence for positive selection in ENAM on the stem dugongid branch where extensive tooth reduction occurred, followed by neutral evolution on the Hydrodamalis branch. Finally, we present a synthetic evolutionary tree for living and fossil sirenians showing several key innovations in the history of this clade including character state changes that parallel those that occurred in the evolutionary history of cetaceans.
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Affiliation(s)
- Mark S Springer
- Department of Biology, University of California, Riverside, CA 92521, USA.
| | - Anthony V Signore
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Johanna L A Paijmans
- Department of Biology, The University of York, Wentworth Way, Heslington, York YO10 5DD, UK
| | - Jorge Vélez-Juarbe
- Department of Mammalogy, Natural History Museum of Los Angeles County, Los Angeles, CA 90007, USA
| | - Daryl P Domning
- Laboratory of Evolutionary Biology, Department of Anatomy, Howard University, Washington, DC 20059, USA; Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Cameron E Bauer
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Kai He
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Lorelei Crerar
- Department of Biology, George Mason University, Fairfax, VA 22030, USA
| | - Paula F Campos
- Center for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark; CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Robert W Meredith
- Department of Biology and Molecular Biology, Montclair State University, Montclair, NJ 07043, USA
| | - John Gatesy
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - Eske Willerslev
- Center for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Ross D E MacPhee
- Department of Mammalogy, American Museum of Natural History, New York, NY 10024, USA
| | - Michael Hofreiter
- Department of Biology, The University of York, Wentworth Way, Heslington, York YO10 5DD, UK; Adaptive and Evolutionary Genomics, Institute for Biochemistry and Biology, Faculty of Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknecht-Strasse 24-24, 14476 Potsdam, Germany
| | - Kevin L Campbell
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
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32
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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: 16] [Impact Index Per Article: 1.8] [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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Wang SK, Hu Y, Yang J, Smith CE, Nunez SM, Richardson AS, Pal S, Samann AC, Hu JCC, Simmer JP. Critical roles for WDR72 in calcium transport and matrix protein removal during enamel maturation. Mol Genet Genomic Med 2015; 3:302-19. [PMID: 26247047 PMCID: PMC4521966 DOI: 10.1002/mgg3.143] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/02/2015] [Accepted: 03/02/2015] [Indexed: 12/19/2022] Open
Abstract
Defects in WDR72 (WD repeat-containing protein 72) cause autosomal recessive hypomaturation amelogenesis imperfecta. We generated and characterized Wdr72-knockout/lacZ-knockin mice to investigate the role of WDR72 in enamel formation. In all analyses, enamel formed by Wdr72 heterozygous mice was indistinguishable from wild-type enamel. Without WDR72, enamel mineral density increased early during the maturation stage but soon arrested. The null enamel layer was only a tenth as hard as wild-type enamel and underwent rapid attrition following eruption. Despite the failure to further mineralize enamel deposited during the secretory stage, ectopic mineral formed on the enamel surface and penetrated into the overlying soft tissue. While the proteins in the enamel matrix were successfully degraded, the digestion products remained inside the enamel. Interactome analysis of WDR72 protein revealed potential interactions with clathrin-associated proteins and involvement in ameloblastic endocytosis. The maturation stage mandibular incisor enamel did not stain with methyl red, indicating that the enamel did not acidify beneath ruffle-ended ameloblasts. Attachment of maturation ameloblasts to the enamel layer was weakened, and SLC24A4, a critical ameloblast calcium transporter, did not localize appropriately along the ameloblast distal membrane. Fewer blood vessels were observed in the papillary layer supporting ameloblasts. Specific WDR72 expression by maturation stage ameloblasts explained the observation that enamel thickness and rod decussation (established during the secretory stage) are normal in the Wdr72 null mice. We conclude that WDR72 serves critical functions specifically during the maturation stage of amelogenesis and is required for both protein removal and enamel mineralization.
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Affiliation(s)
- Shih-Kai Wang
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry 1210 Eisenhower Pl., Ann Arbor, Michigan, 48108
| | - Yuanyuan Hu
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry 1210 Eisenhower Pl., Ann Arbor, Michigan, 48108
| | - Jie Yang
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry 1210 Eisenhower Pl., Ann Arbor, Michigan, 48108 ; Department of Pediatric Dentistry, School and Hospital of Stomatology, Peking University 22 South Avenue Zhongguancun, Haidian District, Beijing, 100081, China
| | - Charles E Smith
- Facility for Electron Microscopy Research, Department of Anatomy and Cell Biology and Faculty of Dentistry, McGill University 3640 University Street, Montreal, Quebec, Canada, H3A 2B2
| | - Stephanie M Nunez
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry 1210 Eisenhower Pl., Ann Arbor, Michigan, 48108
| | - Amelia S Richardson
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry 1210 Eisenhower Pl., Ann Arbor, Michigan, 48108
| | - Soumya Pal
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry 1210 Eisenhower Pl., Ann Arbor, Michigan, 48108
| | - Andrew C Samann
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry 1210 Eisenhower Pl., Ann Arbor, Michigan, 48108
| | - Jan C-C Hu
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry 1210 Eisenhower Pl., Ann Arbor, Michigan, 48108
| | - James P Simmer
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry 1210 Eisenhower Pl., Ann Arbor, Michigan, 48108
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Ekdale EG, Deméré TA, Berta A. Vascularization of the gray whale palate (Cetacea, Mysticeti, Eschrichtius robustus): soft tissue evidence for an alveolar source of blood to baleen. Anat Rec (Hoboken) 2015; 298:691-702. [PMID: 25663479 DOI: 10.1002/ar.23119] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/31/2014] [Accepted: 09/02/2014] [Indexed: 11/08/2022]
Abstract
The origin of baleen in mysticetes heralded a major transition during cetacean evolution. Extant mysticetes are edentulous in adulthood, but rudimentary teeth develop in utero within open maxillary and mandibular alveolar grooves. The teeth are resorbed prenatally and the alveolar grooves close as baleen germ develops. Arteries supplying blood to highly vascularized epithelial tissue from which baleen develops pass through lateral nutrient foramina in the area of the embryonic alveolar grooves and rudimentary teeth. Those vessels are hypothesized to be branches of the superior alveolar artery, but branches of the greater palatine arteries may play a role in the baleen vascularization. Through a combination of latex injection, CT, and traditional dissection of the palate of a neonatal gray whale (Eschrichtius robustus), we confirm that the baleen receives blood from vessels within the superior alveolar canal via the lateral foramina. The greater palatine artery is restricted to its own passage with no connections to the baleen. This study has implications for the presence of baleen in extinct taxa by identifying the vessels and bony canals that supply blood to the epithelium from which baleen develops. The results indicate that the lateral foramina in edentulous mysticete fossils are bony correlates for the presence of baleen, and the results can be used to help identify bony canals and foramina that have been used to reconstruct baleen in extinct mysticetes that retained teeth in adulthood. Further comparisons are made with mammals that also possess oral keratin structures, including ruminants, ornithorhynchid monotremes, and sirenians.
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Affiliation(s)
- Eric G Ekdale
- Department of Biology, San Diego State University, San Diego, California; Department of Paleontology, San Diego Natural History Museum, San Diego, California
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Meredith RW, Zhang G, Gilbert MTP, Jarvis ED, Springer MS. Evidence for a single loss of mineralized teeth in the common avian ancestor. Science 2014; 346:1254390. [DOI: 10.1126/science.1254390] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Gao J, Ruan J, Gao L. Excessive fluoride reducesFoxo1expression in dental epithelial cells of the rat incisor. Eur J Oral Sci 2014; 122:317-23. [DOI: 10.1111/eos.12148] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jianghong Gao
- Department of Oral Prevention; School of Stomatology; Xi'an Jiaotong University; Xi'an Shaanxi China
| | - Jianping Ruan
- Department of Oral Prevention; School of Stomatology; Xi'an Jiaotong University; Xi'an Shaanxi China
| | - Liping Gao
- Department of Oral Prevention; School of Stomatology; Xi'an Jiaotong University; Xi'an Shaanxi China
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37
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Kim DS, Wang Y, Oh HJ, Lee K, Hahn Y. Frequent loss and alteration of the MOXD2 gene in catarrhines and whales: a possible connection with the evolution of olfaction. PLoS One 2014; 9:e104085. [PMID: 25102179 PMCID: PMC4125168 DOI: 10.1371/journal.pone.0104085] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 07/08/2014] [Indexed: 11/18/2022] Open
Abstract
The MOXD2 gene encodes a membrane-bound monooxygenase similar to dopamine-β-hydroxylase, and has been proposed to be associated with olfaction. In this study, we analyzed MOXD2 genes from 64 mammalian species, and identified loss-of-function mutations in apes (humans, Sumatran and Bornean orangutans, and five gibbon species from the four major gibbon genera), toothed whales (killer whales, bottlenose dolphins, finless porpoises, baijis, and sperm whales), and baleen whales (minke whales and fin whales). We also identified a shared 13-nt deletion in the last exon of Old World cercopithecine monkeys that results in conversion of a membrane-bound protein to a soluble form. We hypothesize that the frequent inactivation and alteration of MOXD2 genes in catarrhines and whales may be associated with the evolution of olfaction in these clades.
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Affiliation(s)
- Dong Seon Kim
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Korea
| | - Yao Wang
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Korea
| | - Hye Ji Oh
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Korea
| | - Kangseok Lee
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Korea
| | - Yoonsoo Hahn
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Korea
- * E-mail:
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Bartlett JD, Simmer JP. Kallikrein-related peptidase-4 (KLK4): role in enamel formation and revelations from ablated mice. Front Physiol 2014; 5:240. [PMID: 25071586 PMCID: PMC4082239 DOI: 10.3389/fphys.2014.00240] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 06/10/2014] [Indexed: 12/26/2022] Open
Abstract
Enamel development occurs in stages. During the secretory stage, a soft protein rich enamel layer is produced that expands to reach its final thickness. During the maturation stage, proteins are removed and the enamel matures into the hardest substance in the body. KLK4 is expressed during the transition from secretory to the maturation stage and its expression continues throughout maturation. KLK4 is a glycosylated chymotrypsin-like serine protease that cleaves enamel matrix proteins prior to their export out of the hardening enamel layer. Mutations in KLK4 can cause autosomal recessive, non-syndromic enamel malformations in humans and mice. Klk4 ablated mice initially have normal-looking teeth with enamel of full thickness. However, the enamel is soft and protein-rich. Three findings are notable from Klk4 ablated mice: first, enamel rods fall from the interrod enamel leaving behind empty holes where the enamel fractures near the underlying dentin surface. Second, the ~10,000 crystallites that normally fuse to form a solid enamel rod fail to grow together in the ablated mice and can fall out of the rods. Third, and most striking, the crystallites grow substantially in width and thickness (a- and b-axis) in the ablated mice until they almost interlock. The crystallites grow in defined enamel rods, but interlocking is prevented presumably because too much protein remains. Conventional thought holds that enamel proteins bind specifically to the sides of enamel crystals to inhibit growth in width and thickness so that the thin, ribbon-like enamel crystallites grow predominantly in length. Results from Klk4 ablated mice demonstrate that this convention requires updating. An alternative mechanism is proposed whereby enamel proteins serve to form a mold or support structure that shapes and orients the mineral ribbons as they grow in length. The remnants of this support structure must be removed by KLK4 so that the crystallites can interlock to form fully hardened enamel.
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Affiliation(s)
- John D Bartlett
- Harvard School of Dental Medicine Boston, MA ; Department of Mineralized Tissue Biology, The Forsyth Institute Cambridge, MA
| | - James P Simmer
- Department of Biological and Material Sciences, University of Michigan School of Dentistry Ann Arbor, MI, USA
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39
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McGowen MR, Gatesy J, Wildman DE. Molecular evolution tracks macroevolutionary transitions in Cetacea. Trends Ecol Evol 2014; 29:336-46. [DOI: 10.1016/j.tree.2014.04.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 04/02/2014] [Accepted: 04/03/2014] [Indexed: 10/25/2022]
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40
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Emerling CA, Springer MS. Eyes underground: regression of visual protein networks in subterranean mammals. Mol Phylogenet Evol 2014; 78:260-70. [PMID: 24859681 DOI: 10.1016/j.ympev.2014.05.016] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Revised: 04/26/2014] [Accepted: 05/05/2014] [Indexed: 11/26/2022]
Abstract
Regressive evolution involves the degeneration of formerly useful structures in a lineage over time, and may be accompanied by the molecular decay of phenotype-specific genes. The mammalian eye has repeatedly undergone degeneration in taxa that occupy dim-light environments including subterranean habitats. Here we assess whether a decrease in the amount of light that reaches the retina is associated with increased regression of retinal genes, whether the phototransduction and visual cycle pathways degrade in a predictable pattern, and if the timing of retinal gene loss is associated with the entrance of mammalian lineages into subterranean environments. Sequence data were obtained from the publically available genomes of the Cape golden mole (Chrysochloris asiatica), naked mole-rat (Heterocephalus glaber) and star-nosed mole (Condylura cristata) for 65 genes associated with phototransduction, the visual cycle, and other retinal functions. Gene sequences were inspected for inactivating mutations and, when present, pseudogene sequences were compared to sequences from subaerial outgroup species. To test whether retinal degeneration is correlated with historical entrances into subterranean environments, estimated dates of retinal gene inactivation were compared to the fossil record and phylogenetic inferences of ancestral fossoriality. Our results show that (1) lower levels of light available to the retina correspond with an increase in the number of retinal pseudogenes, (2) retinal protein networks generally degrade in a predictable manner, although the extensive loss of cone phototransduction genes in Heterocephalus raises further questions regarding SWS1-cone monochromacy versus functional rod monochromacy in this species, and (3) inactivation dates of retinal genes usually post-date inferred entrances into subterranean habitats.
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Affiliation(s)
- Christopher A Emerling
- Department of Biology, University of California Riverside, 900 University Ave, Riverside, CA 92521, United States.
| | - Mark S Springer
- Department of Biology, University of California Riverside, 900 University Ave, Riverside, CA 92521, United States.
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41
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Horvath JE, Ramachandran GL, Fedrigo O, Nielsen WJ, Babbitt CC, St Clair EM, Pfefferle LW, Jernvall J, Wray GA, Wall CE. Genetic comparisons yield insight into the evolution of enamel thickness during human evolution. J Hum Evol 2014; 73:75-87. [PMID: 24810709 DOI: 10.1016/j.jhevol.2014.01.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 10/29/2013] [Accepted: 01/09/2014] [Indexed: 12/29/2022]
Abstract
Enamel thickness varies substantially among extant hominoids and is a key trait with significance for interpreting dietary adaptation, life history trajectory, and phylogenetic relationships. There is a strong link in humans between enamel formation and mutations in the exons of the four genes that code for the enamel matrix proteins and the associated protease. The evolution of thick enamel in humans may have included changes in the regulation of these genes during tooth development. The cis-regulatory region in the 5' flank (upstream non-coding region) of MMP20, which codes for enamelysin, the predominant protease active during enamel secretion, has previously been shown to be under strong positive selection in the lineages leading to both humans and chimpanzees. Here we examine evidence for positive selection in the 5' flank and 3' flank of AMELX, AMBN, ENAM, and MMP20. We contrast the human sequence changes with other hominoids (chimpanzees, gorillas, orangutans, gibbons) and rhesus macaques (outgroup), a sample comprising a range of enamel thickness. We find no evidence for positive selection in the protein-coding regions of any of these genes. In contrast, we find strong evidence for positive selection in the 5' flank region of MMP20 and ENAM along the lineage leading to humans, and in both the 5' flank and 3' flank regions of MMP20 along the lineage leading to chimpanzees. We also identify putative transcription factor binding sites overlapping some of the species-specific nucleotide sites and we refine which sections of the up- and downstream putative regulatory regions are most likely to harbor important changes. These non-coding changes and their potential for differential regulation by transcription factors known to regulate tooth development may offer insight into the mechanisms that allow for rapid evolutionary changes in enamel thickness across closely-related species, and contribute to our understanding of the enamel phenotype in hominoids.
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Affiliation(s)
- Julie E Horvath
- North Carolina Museum of Natural Sciences, Nature Research Center, Raleigh, NC 27601, USA; Department of Biology, North Carolina Central University, Durham, NC 27707, USA; Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA; Duke Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
| | | | - Olivier Fedrigo
- Duke Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
| | | | - Courtney C Babbitt
- Duke Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA; Department of Biology, Duke University, Durham, NC 27708, USA
| | | | | | - Jukka Jernvall
- Institute for Biotechnology, University of Helsinki, Helsinki, Finland
| | - Gregory A Wray
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA; Duke Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA; Department of Biology, Duke University, Durham, NC 27708, USA
| | - Christine E Wall
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.
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Chaussain C, Bouazza N, Gasse B, Laffont AG, Opsahl Vital S, Davit-Béal T, Moulis E, Chabadel O, Hennequin M, Courson F, Droz D, Vaysse F, Laboux O, Tassery H, Carel JC, Alcais A, Treluyer JM, Beldjord C, Sire JY. Dental caries and enamelin haplotype. J Dent Res 2014; 93:360-5. [PMID: 24487377 DOI: 10.1177/0022034514522060] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In the literature, the enamelin gene ENAM has been repeatedly designated as a possible candidate for caries susceptibility. Here, we checked whether ENAM variants could increase caries susceptibility. To this aim, we sequenced coding exons and exon-intron boundaries of ENAM in 250 children with a severe caries phenotype and in 149 caries-free patients from 9 French hospital groups. In total, 23 single-nucleotide polymorphisms (SNPs) were found, but none appeared to be responsible for a direct change of ENAM function. Six SNPs had a high minor allele frequency (MAF) and 6 others were identified for the first time. Statistical and evolutionary analyses showed that none of these SNPs was associated with caries susceptibility or caries protection when studied separately and challenged with environmental factors. However, haplotype interaction analysis showed that the presence, in a same variant, of 2 exonic SNPs (rs7671281 and rs3796704; MAF 0.12 and 0.10, respectively), both changing an amino acid in the protein region encoded by exon 10 (p.I648T and p.R763Q, respectively), increased caries susceptibility 2.66-fold independent of the environmental risk factors. These findings support ENAM as a gene candidate for caries susceptibility in the studied population.
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Affiliation(s)
- C Chaussain
- AP-HP, Service Odontologie Bretonneau - Louis Mourier HUPNVS and Centre de référence des maladies du métabolisme du phosphore et du calcium, Paris, France
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Yim HS, Cho YS, Guang X, Kang SG, Jeong JY, Cha SS, Oh HM, Lee JH, Yang EC, Kwon KK, Kim YJ, Kim TW, Kim W, Jeon JH, Kim SJ, Choi DH, Jho S, Kim HM, Ko J, Kim H, Shin YA, Jung HJ, Zheng Y, Wang Z, Chen Y, Chen M, Jiang A, Li E, Zhang S, Hou H, Kim TH, Yu L, Liu S, Ahn K, Cooper J, Park SG, Hong CP, Jin W, Kim HS, Park C, Lee K, Chun S, Morin PA, O'Brien SJ, Lee H, Kimura J, Moon DY, Manica A, Edwards J, Kim BC, Kim S, Wang J, Bhak J, Lee HS, Lee JH. Minke whale genome and aquatic adaptation in cetaceans. Nat Genet 2013; 46:88-92. [PMID: 24270359 DOI: 10.1038/ng.2835] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 11/01/2013] [Indexed: 01/14/2023]
Abstract
The shift from terrestrial to aquatic life by whales was a substantial evolutionary event. Here we report the whole-genome sequencing and de novo assembly of the minke whale genome, as well as the whole-genome sequences of three minke whales, a fin whale, a bottlenose dolphin and a finless porpoise. Our comparative genomic analysis identified an expansion in the whale lineage of gene families associated with stress-responsive proteins and anaerobic metabolism, whereas gene families related to body hair and sensory receptors were contracted. Our analysis also identified whale-specific mutations in genes encoding antioxidants and enzymes controlling blood pressure and salt concentration. Overall the whale-genome sequences exhibited distinct features that are associated with the physiological and morphological changes needed for life in an aquatic environment, marked by resistance to physiological stresses caused by a lack of oxygen, increased amounts of reactive oxygen species and high salt levels.
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Affiliation(s)
- Hyung-Soon Yim
- 1] Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea. [2]
| | - Yun Sung Cho
- 1] Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea. [2]
| | - Xuanmin Guang
- 1] Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China. [2]
| | - Sung Gyun Kang
- 1] Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea. [2] Department of Marine Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Jae-Yeon Jeong
- 1] Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea. [2] Department of Marine Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Sun-Shin Cha
- 1] Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea. [2] Department of Marine Biotechnology, University of Science and Technology, Daejeon, Republic of Korea. [3] Ocean Science and Technology School, Korea Maritime University, Busan, Republic of Korea
| | - Hyun-Myung Oh
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
| | - Jae-Hak Lee
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
| | - Eun Chan Yang
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
| | - Kae Kyoung Kwon
- 1] Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea. [2] Department of Marine Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Yun Jae Kim
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
| | - Tae Wan Kim
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
| | - Wonduck Kim
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
| | - Jeong Ho Jeon
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
| | - Sang-Jin Kim
- 1] Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea. [2] Department of Marine Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Dong Han Choi
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
| | - Sungwoong Jho
- Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea
| | - Hak-Min Kim
- Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea
| | - Junsu Ko
- Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea
| | - Hyunmin Kim
- Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea
| | - Young-Ah Shin
- Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea
| | - Hyun-Ju Jung
- Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea
| | - Yuan Zheng
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Zhuo Wang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Yan Chen
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Ming Chen
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Awei Jiang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Erli Li
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Shu Zhang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Haolong Hou
- Shaanxi Yulin Energy Group Co. Ltd., Yulin, Shaanxi, China
| | - Tae Hyung Kim
- Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea
| | - Lili Yu
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Sha Liu
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Kung Ahn
- Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea
| | - Jesse Cooper
- Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea
| | - Sin-Gi Park
- Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea
| | - Chang Pyo Hong
- Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea
| | - Wook Jin
- Department of Molecular Medicine, School of Medicine, Gachon University, Incheon, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, Republic of Korea
| | - Chankyu Park
- Laboratory of Genome Biology, Department of Animal Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Kyooyeol Lee
- Laboratory of Genome Biology, Department of Animal Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Sung Chun
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Phillip A Morin
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, California, USA
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
| | - Hang Lee
- College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jumpei Kimura
- Department of Anatomy and Cell Biology, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Dae Yeon Moon
- Marine Biodiversity Institute of Korea (MABIK), Ministry of Ocean and Fisheries, Sejong, Republic of Korea
| | - Andrea Manica
- Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Jeremy Edwards
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Byung Chul Kim
- Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea
| | - Sangsoo Kim
- School of Systems Biomedical Science, Soongsil University, Seoul, Republic of Korea
| | - Jun Wang
- 1] Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China. [2] Department of Biology, University of Copenhagen, Copenhagen, Denmark. [3] King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jong Bhak
- 1] Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea. [2] Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea. [3] Program in Nano Science and Technology, Department of Transdisciplinary Studies, Seoul National University, Suwon, Republic of Korea. [4] Advanced Institutes of Convergence Technology Nano Science and Technology, Suwon, Republic of Korea
| | - Hyun Sook Lee
- 1] Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea. [2] Department of Marine Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Jung-Hyun Lee
- 1] Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea. [2] Department of Marine Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
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Bartlett JD. Dental enamel development: proteinases and their enamel matrix substrates. ISRN DENTISTRY 2013; 2013:684607. [PMID: 24159389 PMCID: PMC3789414 DOI: 10.1155/2013/684607] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 07/15/2013] [Indexed: 12/31/2022]
Abstract
This review focuses on recent discoveries and delves in detail about what is known about each of the proteins (amelogenin, ameloblastin, and enamelin) and proteinases (matrix metalloproteinase-20 and kallikrein-related peptidase-4) that are secreted into the enamel matrix. After an overview of enamel development, this review focuses on these enamel proteins by describing their nomenclature, tissue expression, functions, proteinase activation, and proteinase substrate specificity. These proteins and their respective null mice and human mutations are also evaluated to shed light on the mechanisms that cause nonsyndromic enamel malformations termed amelogenesis imperfecta. Pertinent controversies are addressed. For example, do any of these proteins have a critical function in addition to their role in enamel development? Does amelogenin initiate crystallite growth, does it inhibit crystallite growth in width and thickness, or does it do neither? Detailed examination of the null mouse literature provides unmistakable clues and/or answers to these questions, and this data is thoroughly analyzed. Striking conclusions from this analysis reveal that widely held paradigms of enamel formation are inadequate. The final section of this review weaves the recent data into a plausible new mechanism by which these enamel matrix proteins support and promote enamel development.
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Affiliation(s)
- John D. Bartlett
- Harvard School of Dental Medicine & Chair, Department of Mineralized Tissue Biology, The Forsyth Institute, 245 First Street, Cambridge MA 02142, USA
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Gasse B, Karayigit E, Mathieu E, Jung S, Garret A, Huckert M, Morkmued S, Schneider C, Vidal L, Hemmerlé J, Sire JY, Bloch-Zupan A. Homozygous and compound heterozygous MMP20 mutations in amelogenesis imperfecta. J Dent Res 2013; 92:598-603. [PMID: 23625376 DOI: 10.1177/0022034513488393] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In this article, we focus on hypomaturation autosomal-recessive-type amelogenesis imperfecta (type IIA2) and describe 2 new causal Matrix metalloproteinase 20 (MMP20) mutations validated in two unrelated families: a missense mutation p.T130I at the expected homozygous state, and a compound heterozygous mutation having the same mutation combined with a nucleotide deletion, leading to a premature stop codon (p.N120fz*2). We characterized the enamel structure of the latter case using scanning electron microscopy analysis and microanalysis (Energy-dispersive X-ray Spectroscopy, EDX) and confirmed the hypomaturation-type amelogenesis imperfecta as identified in the clinical diagnosis. The mineralized content was slightly decreased, with magnesium substituting for calcium in the crystal structure. The anomalies affected enamel with minimal inter-rod enamel present and apatite crystals perpendicular to the enamel prisms, suggesting a possible new role for MMP20 in enamel formation.
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Affiliation(s)
- B Gasse
- Research group Evolution & Développement du Squelette-EDS, UMR 7138-SAE, Université Pierre et Marie Curie, Paris, France
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Meredith RW, Gatesy J, Emerling CA, York VM, Springer MS. Rod monochromacy and the coevolution of cetacean retinal opsins. PLoS Genet 2013; 9:e1003432. [PMID: 23637615 PMCID: PMC3630094 DOI: 10.1371/journal.pgen.1003432] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 02/15/2013] [Indexed: 01/02/2023] Open
Abstract
Cetaceans have a long history of commitment to a fully aquatic lifestyle that extends back to the Eocene. Extant species have evolved a spectacular array of adaptations in conjunction with their deployment into a diverse array of aquatic habitats. Sensory systems are among those that have experienced radical transformations in the evolutionary history of this clade. In the case of vision, previous studies have demonstrated important changes in the genes encoding rod opsin (RH1), short-wavelength sensitive opsin 1 (SWS1), and long-wavelength sensitive opsin (LWS) in selected cetaceans, but have not examined the full complement of opsin genes across the complete range of cetacean families. Here, we report protein-coding sequences for RH1 and both color opsin genes (SWS1, LWS) from representatives of all extant cetacean families. We examine competing hypotheses pertaining to the timing of blue shifts in RH1 relative to SWS1 inactivation in the early history of Cetacea, and we test the hypothesis that some cetaceans are rod monochomats. Molecular evolutionary analyses contradict the "coastal" hypothesis, wherein SWS1 was pseudogenized in the common ancestor of Cetacea, and instead suggest that RH1 was blue-shifted in the common ancestor of Cetacea before SWS1 was independently knocked out in baleen whales (Mysticeti) and in toothed whales (Odontoceti). Further, molecular evidence implies that LWS was inactivated convergently on at least five occasions in Cetacea: (1) Balaenidae (bowhead and right whales), (2) Balaenopteroidea (rorquals plus gray whale), (3) Mesoplodon bidens (Sowerby's beaked whale), (4) Physeter macrocephalus (giant sperm whale), and (5) Kogia breviceps (pygmy sperm whale). All of these cetaceans are known to dive to depths of at least 100 m where the underwater light field is dim and dominated by blue light. The knockout of both SWS1 and LWS in multiple cetacean lineages renders these taxa rod monochromats, a condition previously unknown among mammalian species.
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Affiliation(s)
- Robert W. Meredith
- Department of Biology, University of California Riverside, Riverside, California, United States of America
- Department of Biology and Molecular Biology, Montclair State University, Montclair, New Jersey, United States of America
| | - John Gatesy
- Department of Biology, University of California Riverside, Riverside, California, United States of America
| | - Christopher A. Emerling
- Department of Biology, University of California Riverside, Riverside, California, United States of America
| | - Vincent M. York
- Department of Biology, University of California Riverside, Riverside, California, United States of America
- Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Mark S. Springer
- Department of Biology, University of California Riverside, Riverside, California, United States of America
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47
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Bradley Shaffer H, Minx P, Warren DE, Shedlock AM, Thomson RC, Valenzuela N, Abramyan J, Amemiya CT, Badenhorst D, Biggar KK, Borchert GM, Botka CW, Bowden RM, Braun EL, Bronikowski AM, Bruneau BG, Buck LT, Capel B, Castoe TA, Czerwinski M, Delehaunty KD, Edwards SV, Fronick CC, Fujita MK, Fulton L, Graves TA, Green RE, Haerty W, Hariharan R, Hernandez O, Hillier LW, Holloway AK, Janes D, Janzen FJ, Kandoth C, Kong L, de Koning APJ, Li Y, Literman R, McGaugh SE, Mork L, O'Laughlin M, Paitz RT, Pollock DD, Ponting CP, Radhakrishnan S, Raney BJ, Richman JM, St John J, Schwartz T, Sethuraman A, Spinks PQ, Storey KB, Thane N, Vinar T, Zimmerman LM, Warren WC, Mardis ER, Wilson RK. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biol 2013; 14:R28. [PMID: 23537068 PMCID: PMC4054807 DOI: 10.1186/gb-2013-14-3-r28] [Citation(s) in RCA: 229] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 03/15/2013] [Accepted: 03/28/2013] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND We describe the genome of the western painted turtle, Chrysemys picta bellii, one of the most widespread, abundant, and well-studied turtles. We place the genome into a comparative evolutionary context, and focus on genomic features associated with tooth loss, immune function, longevity, sex differentiation and determination, and the species' physiological capacities to withstand extreme anoxia and tissue freezing. RESULTS Our phylogenetic analyses confirm that turtles are the sister group to living archosaurs, and demonstrate an extraordinarily slow rate of sequence evolution in the painted turtle. The ability of the painted turtle to withstand complete anoxia and partial freezing appears to be associated with common vertebrate gene networks, and we identify candidate genes for future functional analyses. Tooth loss shares a common pattern of pseudogenization and degradation of tooth-specific genes with birds, although the rate of accumulation of mutations is much slower in the painted turtle. Genes associated with sex differentiation generally reflect phylogeny rather than convergence in sex determination functionality. Among gene families that demonstrate exceptional expansions or show signatures of strong natural selection, immune function and musculoskeletal patterning genes are consistently over-represented. CONCLUSIONS Our comparative genomic analyses indicate that common vertebrate regulatory networks, some of which have analogs in human diseases, are often involved in the western painted turtle's extraordinary physiological capacities. As these regulatory pathways are analyzed at the functional level, the painted turtle may offer important insights into the management of a number of human health disorders.
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Affiliation(s)
- H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095-1606, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA 90095-1496, USA
| | - Patrick Minx
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Daniel E Warren
- Department of Biology, Saint Louis University, St Louis, MO 63103, USA
| | - Andrew M Shedlock
- College of Charleston Biology Department and Grice Marine Laboratory, Charleston, SC 29424, USA
- Medical University of South Carolina College of Graduate Studies and Center for Marine Biomedicine and Environmental Sciences, Charleston, SC 29412, USA
| | - Robert C Thomson
- Department of Biology, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - John Abramyan
- Faculty of Dentistry, Life Sciences Institute University of British Columbia, Vancouver BC, Canada
| | - Chris T Amemiya
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101 USA
| | - Daleen Badenhorst
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Kyle K Biggar
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, ON, Canada K1S 5B6, Canada
| | - Glen M Borchert
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
- Department of Biological Sciences, Life Sciences Building, University of South Alabama, Mobile, AL 36688-0002, USA
| | | | - Rachel M Bowden
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL 32611 USA
| | - Anne M Bronikowski
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Benoit G Bruneau
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
- Cardiovascular Research Institute and Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Leslie T Buck
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada M5S 3G5, Canada
| | - Blanche Capel
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Todd A Castoe
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Mike Czerwinski
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Kim D Delehaunty
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Catrina C Fronick
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Matthew K Fujita
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Lucinda Fulton
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Tina A Graves
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Richard E Green
- Baskin School of Engineering University of California, Santa Cruz Santa Cruz, CA 95064, USA
| | - Wilfried Haerty
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Henry Wellcome Building of Gene Function, University of Oxford, Oxford, OX13PT, UK
| | - Ramkumar Hariharan
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Poojapura, Thycaud P.O, Thiruvananthapuram, Kerala 695014, India
| | - Omar Hernandez
- FUDECI, Fundación para el Desarrollo de las Ciencias Físicas, Matemáticas y Naturales. Av, Universidad, Bolsa a San Francisco, Palacio de Las Academias, Caracas, Venezuela
| | - LaDeana W Hillier
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Alisha K Holloway
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Daniel Janes
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Fredric J Janzen
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Cyriac Kandoth
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Lesheng Kong
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Henry Wellcome Building of Gene Function, University of Oxford, Oxford, OX13PT, UK
| | - AP Jason de Koning
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Yang Li
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Henry Wellcome Building of Gene Function, University of Oxford, Oxford, OX13PT, UK
| | - Robert Literman
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | | | - Lindsey Mork
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Michelle O'Laughlin
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Ryan T Paitz
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - David D Pollock
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Chris P Ponting
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Henry Wellcome Building of Gene Function, University of Oxford, Oxford, OX13PT, UK
| | - Srihari Radhakrishnan
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Bioinformatics and Computational Biology Laboratory, Iowa State University, Ames, IA 50011, USA
| | - Brian J Raney
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
| | - Joy M Richman
- Faculty of Dentistry, Life Sciences Institute University of British Columbia, Vancouver BC, Canada
| | - John St John
- Baskin School of Engineering University of California, Santa Cruz Santa Cruz, CA 95064, USA
| | - Tonia Schwartz
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Bioinformatics and Computational Biology Laboratory, Iowa State University, Ames, IA 50011, USA
| | - Arun Sethuraman
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Bioinformatics and Computational Biology Laboratory, Iowa State University, Ames, IA 50011, USA
| | - Phillip Q Spinks
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095-1606, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA 90095-1496, USA
| | - Kenneth B Storey
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, ON, Canada K1S 5B6, Canada
| | - Nay Thane
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Tomas Vinar
- Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynska Dolina, Bratislava 84248, Slovakia
| | - Laura M Zimmerman
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Wesley C Warren
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Elaine R Mardis
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Richard K Wilson
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
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Meredith RW, Gatesy J, Springer MS. Molecular decay of enamel matrix protein genes in turtles and other edentulous amniotes. BMC Evol Biol 2013; 13:20. [PMID: 23342979 PMCID: PMC3562159 DOI: 10.1186/1471-2148-13-20] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 01/16/2013] [Indexed: 11/20/2022] Open
Abstract
Background Secondary edentulism (toothlessness) has evolved on multiple occasions in amniotes including several mammalian lineages (pangolins, anteaters, baleen whales), birds, and turtles. All edentulous amniote clades have evolved from ancestors with enamel-capped teeth. Previous studies have documented the molecular decay of tooth-specific genes in edentulous mammals, all of which lost their teeth in the Cenozoic, and birds, which lost their teeth in the Cretaceous. By contrast with mammals and birds, tooth loss in turtles occurred in the Jurassic (201.6-145.5 Ma), providing an extended time window for tooth gene degradation in this clade. The release of the painted turtle and Chinese softshell turtle genomes provides an opportunity to recover the decayed remains of tooth-specific genes in Testudines. Results We queried available genomes of Testudines (Chrysemys picta [painted turtle], Pelodiscus sinensis [Chinese softshell turtle]), Aves (Anas platyrhynchos [duck], Gallus gallus [chicken], Meleagris gallopavo [turkey], Melopsittacus undulatus [budgerigar], Taeniopygia guttata [zebra finch]), and enamelless mammals (Orycteropus afer [aardvark], Choloepus hoffmanni [Hoffmann’s two-toed sloth], Dasypus novemcinctus [nine-banded armadillo]) for remnants of three enamel matrix protein (EMP) genes with putative enamel-specific functions. Remnants of the AMBN and ENAM genes were recovered in Chrysemys and retain their original synteny. Remnants of AMEL were recovered in both testudines, although there are no shared frameshifts. We also show that there are inactivated copies of AMBN, AMEL and ENAM in representatives of divergent avian lineages including Galloanserae, Passeriformes, and Psittaciformes, and that there are shared frameshift mutations in all three genes that predate the basal split in Neognathae. Among enamelless mammals, all three EMP genes exhibit inactivating mutations in Orycteropus and Choloepus. Conclusions Our results highlight the power of combining fossil and genomic evidence to decipher macroevolutionary transitions and characterize the functional range of different loci involved in tooth development. The fossil record and phylogenetics combine to predict the occurrence of molecular fossils of tooth-specific genes in the genomes of edentulous amniotes, and in every case these molecular fossils have been discovered. The widespread occurrence of EMP pseudogenes in turtles, birds, and edentulous/enamelless mammals also provides compelling evidence that in amniotes, the only unique, non-redundant function of these genes is in enamel formation.
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Affiliation(s)
- Robert W Meredith
- Department of Biology, University of California, Riverside, CA 92521, USA
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49
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Bodyweight assessment of enamelin null mice. BIOMED RESEARCH INTERNATIONAL 2012; 2013:246861. [PMID: 23509695 PMCID: PMC3591218 DOI: 10.1155/2013/246861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 10/17/2012] [Accepted: 10/22/2012] [Indexed: 11/18/2022]
Abstract
The Enam null mice appear to be smaller than wild-type mice, which prompted the hypothesis that enamel defects negatively influence nutritional intake and bodyweight gain (BWG). We compared the BWG of Enam−/− and wild-type mice from birth (D0) to Day 42 (D42). Wild-type (WT) and Enam−/− (N) mice were given either hard chow (HC) or soft chow (SC). Four experimental groups were studied: WTHC, WTSC, NHC, and NSC. The mother's bodyweight (DBW) and the average litter bodyweight (ALBW) were obtained from D0 to D21. After D21, the pups were separated from the mother and provided the same type of food. Litter bodyweights were measured until D42. ALBW was compared at 7-day intervals using one-way ANOVA, while the influence of DBW on ALBW was analyzed by mixed-model analyses. The ALBW of Enam−/− mice maintained on hard chow (NHC) was significantly lower than the two WT groups at D21 and the differences persisted into young adulthood. The ALBW of Enam−/− mice maintained on soft chow (NSC) trended lower, but was not significantly different than that of the WT groups. We conclude that genotype, which affects enamel integrity, and food hardness influence bodyweight gain in postnatal and young adult mice.
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50
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Hu JCC, Chan HC, Simmer SG, Seymen F, Richardson AS, Hu Y, Milkovich RN, Estrella NMRP, Yildirim M, Bayram M, Chen CF, Simmer JP. Amelogenesis imperfecta in two families with defined AMELX deletions in ARHGAP6. PLoS One 2012; 7:e52052. [PMID: 23251683 PMCID: PMC3522662 DOI: 10.1371/journal.pone.0052052] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 11/12/2012] [Indexed: 11/18/2022] Open
Abstract
Amelogenesis imperfecta (AI) is a group of inherited conditions featuring isolated enamel malformations. About 5% of AI cases show an X-linked pattern of inheritance, which are caused by mutations in AMELX. In humans there are two, non-allelic amelogenin genes: AMELX (Xp22.3) and AMELY (Yp11.2). About 90% of amelogenin expression is from AMELX, which is nested within intron 1 of the gene encoding Rho GTPase activating protein 6 (ARHGAP6). We recruited two AI families and determined that their disease-causing mutations were partial deletions in ARHGAP6 that completely deleted AMELX. Affected males in both families had a distinctive enamel phenotype resembling "snow-capped" teeth. The 96,240 bp deletion in family 1 was confined to intron 1 of ARHGAP6 (g.302534_398773del96240), but removed alternative ARHGAP6 promoters 1c and 1d. Analyses of developing teeth in mice showed that ARHGAP6 is not expressed from these promoters in ameloblasts. The 52,654 bp deletion in family 2 (g.363924_416577del52654insA) removed ARHGAP6 promoter 1d and exon 2, precluding normal expression of ARHGAP6. The male proband of family 2 had slightly thinner enamel with greater surface roughness, but exhibited the same pattern of enamel malformations characteristic of males in family 1, which themselves showed minor variations in their enamel phenotypes. We conclude that the enamel defects in both families were caused by amelogenin insufficiency, that deletion of AMELX results in males with a characteristic snow-capped enamel phenotype, and failed ARHGAP6 expression did not appreciably alter the severity of enamel defects when AMELX was absent.
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Affiliation(s)
- Jan C-C Hu
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, Ann Arbor, Michigan, USA.
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