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Contrasting evolutionary dynamics of the developmental regulator PAX9, among bats, with evidence for a novel post-transcriptional regulatory mechanism.

Phillips CD, Butler B, Fondon JW, Mantilla-Meluk H, Baker RJ - PLoS ONE (2013)

Bottom Line: Morphological evolution can be the result of natural selection favoring modification of developmental signaling pathways.Although a connection between morphology and binding element frequency was not apparent, results indicate this regulation would vary among craniofacially divergent bat species, but be static among conserved species.The presence of Musashi-binding elements within PAX9 of all mammals examined, chicken, zebrafish, and the fly homolog of PAX9, indicates this regulatory mechanism is ancient, originating basal to much of the animal phylogeny.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America. caleb.phillips@ttu.edu

ABSTRACT
Morphological evolution can be the result of natural selection favoring modification of developmental signaling pathways. However, little is known about the genetic basis of such phenotypic diversity. Understanding these mechanisms is difficult for numerous reasons, yet studies in model organisms often provide clues about the major developmental pathways involved. The paired-domain gene, PAX9, is known to be a key regulator of development, particularly of the face and teeth. In this study, using a comparative genetics approach, we investigate PAX9 molecular evolution among mammals, focusing on craniofacially diversified (Phyllostomidae) and conserved (Vespertilionidae) bat families, and extend our comparison to other orders of mammal. Open-reading frame analysis disclosed signatures of selection, in which a small percentage of residues vary, and lineages acquire different combinations of variation through recurrent substitution and lineage specific changes. A few instances of convergence for specific residues were observed between morphologically convergent bat lineages. Bioinformatic analysis for unknown PAX9 regulatory motifs indicated a novel post-transcriptional regulatory mechanism involving a Musashi protein. This regulation was assessed through fluorescent reporter assays and gene knockdowns. Results are compatible with the hypothesis that the number of Musashi binding-elements in PAX9 mRNA proportionally regulates protein translation rate. Although a connection between morphology and binding element frequency was not apparent, results indicate this regulation would vary among craniofacially divergent bat species, but be static among conserved species. Under this model, Musashi's regulatory control of alternative human PAX9 isoforms would also vary. The presence of Musashi-binding elements within PAX9 of all mammals examined, chicken, zebrafish, and the fly homolog of PAX9, indicates this regulatory mechanism is ancient, originating basal to much of the animal phylogeny.

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Patterns of PAX9 open-reading frame evolution.Although under tight purifying selection, PAX9 exhibits patterns of saturation and recurrent substitution contingent on the level of comparison (amino acid versus nucleotide) as well as the amount of evolutionary time considered in the data. A) and B) display the pairwise nucleotide and predicted amino acid differences among orders regressed against tmrca, respectively. C) and D) show similar plots, but among species from the families Phyllostomidae, Vespertilionidae and Miniopteridae, and the order Primates. E) Confidence in PSIPRED secondary structure prediction (greater confidence represented by larger bars) for each of the 341 residues of Pax9, and shading demarks exons. Directly below this histogram is the structural prediction in which white bars represent coiled structures and black represent helical regions. The solid grey bar at the bottom defines the limits of the paired-binding domain described by [7]. Vertical lines pointing to each codon position in the histogram indicate positions that vary across the mammalian taxa examined, and taller lines demark sights inferred to have accumulated recurrent substitutions. The number of inferred substitutions at these sights from left to right are as follows: 3, 2, 3, 2, 7, 4, 3, 4, 8, 6, 3, 2, 4, 4, 2, 3, 2, and 5. F) Reticulation network based on predicted amino acid translations. Closed loops in the network indicate homoplasies, and edge thickness is in proportion to bootstrap support.
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pone-0057649-g003: Patterns of PAX9 open-reading frame evolution.Although under tight purifying selection, PAX9 exhibits patterns of saturation and recurrent substitution contingent on the level of comparison (amino acid versus nucleotide) as well as the amount of evolutionary time considered in the data. A) and B) display the pairwise nucleotide and predicted amino acid differences among orders regressed against tmrca, respectively. C) and D) show similar plots, but among species from the families Phyllostomidae, Vespertilionidae and Miniopteridae, and the order Primates. E) Confidence in PSIPRED secondary structure prediction (greater confidence represented by larger bars) for each of the 341 residues of Pax9, and shading demarks exons. Directly below this histogram is the structural prediction in which white bars represent coiled structures and black represent helical regions. The solid grey bar at the bottom defines the limits of the paired-binding domain described by [7]. Vertical lines pointing to each codon position in the histogram indicate positions that vary across the mammalian taxa examined, and taller lines demark sights inferred to have accumulated recurrent substitutions. The number of inferred substitutions at these sights from left to right are as follows: 3, 2, 3, 2, 7, 4, 3, 4, 8, 6, 3, 2, 4, 4, 2, 3, 2, and 5. F) Reticulation network based on predicted amino acid translations. Closed loops in the network indicate homoplasies, and edge thickness is in proportion to bootstrap support.

Mentions: In order to characterize the distribution genetic variation over evolutionary time, pairwise nucleotide and predicted amino acids differences at different taxonomic levels were regressed against tmrca (Figure 3a–d). The regression plots indicated saturation at the nucleotide level among orders (manifested as a weak linear relationship between pairwise differences and divergence time), but not within comparisons among bat families and among primates. Conversely, amino acid evolution was not heavily saturated in comparisons between orders, or through comparisons within bats and within primates.


Contrasting evolutionary dynamics of the developmental regulator PAX9, among bats, with evidence for a novel post-transcriptional regulatory mechanism.

Phillips CD, Butler B, Fondon JW, Mantilla-Meluk H, Baker RJ - PLoS ONE (2013)

Patterns of PAX9 open-reading frame evolution.Although under tight purifying selection, PAX9 exhibits patterns of saturation and recurrent substitution contingent on the level of comparison (amino acid versus nucleotide) as well as the amount of evolutionary time considered in the data. A) and B) display the pairwise nucleotide and predicted amino acid differences among orders regressed against tmrca, respectively. C) and D) show similar plots, but among species from the families Phyllostomidae, Vespertilionidae and Miniopteridae, and the order Primates. E) Confidence in PSIPRED secondary structure prediction (greater confidence represented by larger bars) for each of the 341 residues of Pax9, and shading demarks exons. Directly below this histogram is the structural prediction in which white bars represent coiled structures and black represent helical regions. The solid grey bar at the bottom defines the limits of the paired-binding domain described by [7]. Vertical lines pointing to each codon position in the histogram indicate positions that vary across the mammalian taxa examined, and taller lines demark sights inferred to have accumulated recurrent substitutions. The number of inferred substitutions at these sights from left to right are as follows: 3, 2, 3, 2, 7, 4, 3, 4, 8, 6, 3, 2, 4, 4, 2, 3, 2, and 5. F) Reticulation network based on predicted amino acid translations. Closed loops in the network indicate homoplasies, and edge thickness is in proportion to bootstrap support.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3585407&req=5

pone-0057649-g003: Patterns of PAX9 open-reading frame evolution.Although under tight purifying selection, PAX9 exhibits patterns of saturation and recurrent substitution contingent on the level of comparison (amino acid versus nucleotide) as well as the amount of evolutionary time considered in the data. A) and B) display the pairwise nucleotide and predicted amino acid differences among orders regressed against tmrca, respectively. C) and D) show similar plots, but among species from the families Phyllostomidae, Vespertilionidae and Miniopteridae, and the order Primates. E) Confidence in PSIPRED secondary structure prediction (greater confidence represented by larger bars) for each of the 341 residues of Pax9, and shading demarks exons. Directly below this histogram is the structural prediction in which white bars represent coiled structures and black represent helical regions. The solid grey bar at the bottom defines the limits of the paired-binding domain described by [7]. Vertical lines pointing to each codon position in the histogram indicate positions that vary across the mammalian taxa examined, and taller lines demark sights inferred to have accumulated recurrent substitutions. The number of inferred substitutions at these sights from left to right are as follows: 3, 2, 3, 2, 7, 4, 3, 4, 8, 6, 3, 2, 4, 4, 2, 3, 2, and 5. F) Reticulation network based on predicted amino acid translations. Closed loops in the network indicate homoplasies, and edge thickness is in proportion to bootstrap support.
Mentions: In order to characterize the distribution genetic variation over evolutionary time, pairwise nucleotide and predicted amino acids differences at different taxonomic levels were regressed against tmrca (Figure 3a–d). The regression plots indicated saturation at the nucleotide level among orders (manifested as a weak linear relationship between pairwise differences and divergence time), but not within comparisons among bat families and among primates. Conversely, amino acid evolution was not heavily saturated in comparisons between orders, or through comparisons within bats and within primates.

Bottom Line: Morphological evolution can be the result of natural selection favoring modification of developmental signaling pathways.Although a connection between morphology and binding element frequency was not apparent, results indicate this regulation would vary among craniofacially divergent bat species, but be static among conserved species.The presence of Musashi-binding elements within PAX9 of all mammals examined, chicken, zebrafish, and the fly homolog of PAX9, indicates this regulatory mechanism is ancient, originating basal to much of the animal phylogeny.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America. caleb.phillips@ttu.edu

ABSTRACT
Morphological evolution can be the result of natural selection favoring modification of developmental signaling pathways. However, little is known about the genetic basis of such phenotypic diversity. Understanding these mechanisms is difficult for numerous reasons, yet studies in model organisms often provide clues about the major developmental pathways involved. The paired-domain gene, PAX9, is known to be a key regulator of development, particularly of the face and teeth. In this study, using a comparative genetics approach, we investigate PAX9 molecular evolution among mammals, focusing on craniofacially diversified (Phyllostomidae) and conserved (Vespertilionidae) bat families, and extend our comparison to other orders of mammal. Open-reading frame analysis disclosed signatures of selection, in which a small percentage of residues vary, and lineages acquire different combinations of variation through recurrent substitution and lineage specific changes. A few instances of convergence for specific residues were observed between morphologically convergent bat lineages. Bioinformatic analysis for unknown PAX9 regulatory motifs indicated a novel post-transcriptional regulatory mechanism involving a Musashi protein. This regulation was assessed through fluorescent reporter assays and gene knockdowns. Results are compatible with the hypothesis that the number of Musashi binding-elements in PAX9 mRNA proportionally regulates protein translation rate. Although a connection between morphology and binding element frequency was not apparent, results indicate this regulation would vary among craniofacially divergent bat species, but be static among conserved species. Under this model, Musashi's regulatory control of alternative human PAX9 isoforms would also vary. The presence of Musashi-binding elements within PAX9 of all mammals examined, chicken, zebrafish, and the fly homolog of PAX9, indicates this regulatory mechanism is ancient, originating basal to much of the animal phylogeny.

Show MeSH
Related in: MedlinePlus