Evolutionary analysis of selective constraints identifies ameloblastin (AMBN) as a potential candidate for amelogenesis imperfecta
Identifieur interne : 000025 ( France/Analysis ); précédent : 000024; suivant : 000026Evolutionary analysis of selective constraints identifies ameloblastin (AMBN) as a potential candidate for amelogenesis imperfecta
Auteurs : Frédéric Delsuc [France] ; Barbara Gasse [France] ; Jean-Yves Sire [France]Source :
- BMC Evolutionary Biology [ 1471-2148 ] ; 2015.
Abstract
Ameloblastin (AMBN) is a phosphorylated, proline/glutamine-rich protein secreted during enamel formation. Previous studies have revealed that this enamel matrix protein was present early in vertebrate evolution and certainly plays important roles during enamel formation although its precise functions remain unclear. We performed evolutionary analyses of AMBN in order to (i) identify residues and motifs important for the protein function, (ii) predict mutations responsible for genetic diseases, and (iii) understand its molecular evolution in mammals.
In silico searches retrieved 56 complete sequences in public databases that were aligned and analyzed computationally. We showed that
AMBN possesses many positions, which have been subjected to strong selective pressure for 200 million years. These positions correspond to several cleavage sites and hydroxylated, O-glycosylated, and phosphorylated residues. We predict that these conserved positions would be potentially responsible for enamel disorder if substituted. Some motifs that were previously identified as potentially important functionally were confirmed, and we found two, highly conserved, new motifs, the function of which should be tested in the near future. This study illustrates the power of evolutionary analyses for characterizing the functional constraints acting on proteins with yet uncharacterized structure.
The online version of this article (doi:10.1186/s12862-015-0431-0) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12862-015-0431-0
PubMed: 26223266
PubMed Central: 4518657
Affiliations:
- France
- Languedoc-Roussillon, Occitanie (région administrative), Île-de-France
- Montpellier, Paris
- Université Pierre-et-Marie-Curie
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PMC:4518657Le document en format XML
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xml:lang="fr">France</country><wicri:regionArea>Institut des Sciences de l’Evolution, UMR 5554, CNRS, IRD, EPHE, Université de Montpellier, Montpellier</wicri:regionArea><placeName><region type="region">Occitanie (région administrative)</region><region type="old region">Languedoc-Roussillon</region><settlement type="city">Montpellier</settlement></placeName></affiliation></author><author><name sortKey="Gasse, Barbara" sort="Gasse, Barbara" uniqKey="Gasse B" first="Barbara" last="Gasse">Barbara Gasse</name><affiliation wicri:level="4"><nlm:aff id="Aff2">Université Pierre et Marie Curie, UMR 7138 Evolution Paris-Seine, Paris, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Université Pierre et Marie Curie, UMR 7138 Evolution Paris-Seine, Paris</wicri:regionArea><placeName><region type="region">Île-de-France</region><region type="old region">Île-de-France</region><settlement type="city">Paris</settlement><settlement type="city">Paris</settlement></placeName><orgName type="university">Université Pierre-et-Marie-Curie</orgName></affiliation></author><author><name sortKey="Sire, Jean Yves" sort="Sire, Jean Yves" uniqKey="Sire J" first="Jean-Yves" last="Sire">Jean-Yves Sire</name><affiliation wicri:level="4"><nlm:aff id="Aff2">Université Pierre et Marie Curie, UMR 7138 Evolution Paris-Seine, Paris, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Université Pierre et Marie Curie, UMR 7138 Evolution Paris-Seine, Paris</wicri:regionArea><placeName><region type="region">Île-de-France</region><region type="old region">Île-de-France</region><settlement type="city">Paris</settlement><settlement type="city">Paris</settlement></placeName><orgName type="university">Université Pierre-et-Marie-Curie</orgName></affiliation></author></analytic><series><title level="j">BMC Evolutionary Biology</title><idno type="eISSN">1471-2148</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Ameloblastin (AMBN) is a phosphorylated, proline/glutamine-rich protein secreted during enamel formation. Previous studies have revealed that this enamel matrix protein was present early in vertebrate evolution and certainly plays important roles during enamel formation although its precise functions remain unclear. We performed evolutionary analyses of AMBN in order to (i) identify residues and motifs important for the protein function, (ii) predict mutations responsible for genetic diseases, and (iii) understand its molecular evolution in mammals.</p></sec><sec><title>Results</title><p>In silico searches retrieved 56 complete sequences in public databases that were aligned and analyzed computationally. We showed that <italic>AMBN</italic> is globally evolving under moderate purifying selection in mammals and contains a strong phylogenetic signal. In addition, our analyses revealed codons evolving under significant positive selection. Evidence for positive selection acting on AMBN was observed in catarrhine primates and the aye-aye. We also found that (i) an additional translation initiation site was recruited in the ancestral placental <italic>AMBN</italic>, (ii) a short exon was duplicated several times in various species including catarrhine primates, and (iii) several polyadenylation sites are present.</p></sec><sec><title>Conclusions</title><p>AMBN possesses many positions, which have been subjected to strong selective pressure for 200 million years. These positions correspond to several cleavage sites and hydroxylated, O-glycosylated, and phosphorylated residues. We predict that these conserved positions would be potentially responsible for enamel disorder if substituted. Some motifs that were previously identified as potentially important functionally were confirmed, and we found two, highly conserved, new motifs, the function of which should be tested in the near future. This study illustrates the power of evolutionary analyses for characterizing the functional constraints acting on proteins with yet uncharacterized structure.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12862-015-0431-0) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Kawasaki, K" uniqKey="Kawasaki K">K Kawasaki</name></author><author><name sortKey="Weiss, Km" uniqKey="Weiss K">KM Weiss</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kawasaki, K" uniqKey="Kawasaki K">K Kawasaki</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sire, J Y" uniqKey="Sire J">J-Y Sire</name></author><author><name sortKey="Delgado, S" uniqKey="Delgado S">S Delgado</name></author><author><name sortKey="Girondot, M" uniqKey="Girondot M">M 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uniqKey="Mcgraw W">WS McGraw</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kelley, Jl" uniqKey="Kelley J">JL Kelley</name></author><author><name sortKey="Swanson, Wj" uniqKey="Swanson W">WJ Swanson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Meredith, Rw" uniqKey="Meredith R">RW Meredith</name></author><author><name sortKey="Gatesy, J" uniqKey="Gatesy J">J Gatesy</name></author><author><name sortKey="Murphy, Wj" uniqKey="Murphy W">WJ Murphy</name></author><author><name sortKey="Ryder, Oa" uniqKey="Ryder O">OA Ryder</name></author><author><name sortKey="Springer, Ms" uniqKey="Springer M">MS Springer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Meredith, Rw" uniqKey="Meredith R">RW Meredith</name></author><author><name sortKey="Zhang, G" uniqKey="Zhang G">G Zhang</name></author><author><name sortKey="Gilbert, Mtp" uniqKey="Gilbert M">MTP Gilbert</name></author><author><name sortKey="Jarvis, Ed" uniqKey="Jarvis E">ED Jarvis</name></author><author><name sortKey="Springer, Ms" uniqKey="Springer M">MS Springer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chun, Y Hp" uniqKey="Chun Y">Y-HP Chun</name></author><author><name sortKey="Yamakoshi, Y" uniqKey="Yamakoshi Y">Y Yamakoshi</name></author><author><name sortKey="Yamakoshi, F" uniqKey="Yamakoshi F">F Yamakoshi</name></author><author><name sortKey="Fukae, M" uniqKey="Fukae M">M Fukae</name></author><author><name sortKey="Hu, Jc C" uniqKey="Hu J">JC-C Hu</name></author><author><name sortKey="Bartlett, Jd" uniqKey="Bartlett J">JD Bartlett</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>France</li></country><region><li>Languedoc-Roussillon</li><li>Occitanie (région administrative)</li><li>Île-de-France</li></region><settlement><li>Montpellier</li><li>Paris</li></settlement><orgName><li>Université Pierre-et-Marie-Curie</li></orgName></list><tree><country name="France"><region name="Occitanie (région administrative)"><name sortKey="Delsuc, Frederic" sort="Delsuc, Frederic" uniqKey="Delsuc F" first="Frédéric" last="Delsuc">Frédéric Delsuc</name></region><name sortKey="Gasse, Barbara" sort="Gasse, Barbara" uniqKey="Gasse B" first="Barbara" last="Gasse">Barbara Gasse</name><name sortKey="Sire, Jean Yves" sort="Sire, Jean Yves" uniqKey="Sire J" first="Jean-Yves" last="Sire">Jean-Yves Sire</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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