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Phylogenetic Patterns of Codon Evolution in the ACTIN-DEPOLYMERIZING FACTOR/COFILIN (ADF/CFL) Gene Family.

Roy-Zokan EM, Dyer KA, Meagher RB - PLoS ONE (2015)

Bottom Line: Estimating the rate of non-synonymous to synonymous mutations (dN/dS) across phylogenetic lineages revealed that the majority of ADF/CFL codon positions were under strong purifying selection, with rare episodic events of accelerated protein evolution.In both plants and animals these instances of accelerated evolution were ADF/CFL subclass specific, and all of the sites under selection were located in regions of the protein that could serve in new functional roles.We suggest these sites may have been important in the functional diversification of ADF/CFL proteins.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, University of Georgia, Athens, Georgia, United States of America.

ABSTRACT
The actin-depolymerizing factor/cofilin (ADF/CFL) gene family encodes a diverse group of relatively small proteins. Once known strictly as modulators of actin filament dynamics, recent research has demonstrated that these proteins are involved in a variety of cellular processes, from signal transduction to the cytonuclear trafficking of actin. In both plant and animal lineages, expression patterns of paralogs in the ADF/CFL gene family vary among tissue types and developmental stages. In this study we use computational approaches to investigate the evolutionary forces responsible for the diversification of the ADF/CFL gene family. Estimating the rate of non-synonymous to synonymous mutations (dN/dS) across phylogenetic lineages revealed that the majority of ADF/CFL codon positions were under strong purifying selection, with rare episodic events of accelerated protein evolution. In both plants and animals these instances of accelerated evolution were ADF/CFL subclass specific, and all of the sites under selection were located in regions of the protein that could serve in new functional roles. We suggest these sites may have been important in the functional diversification of ADF/CFL proteins.

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Bayesian phylogenetic analysis of the animal ADF/CFL gene family.The three ADF/CFL classes are highlighted in boxes. Species designation are as follows: Hs, Homo sapiens; Mm, Mus musculus; Ss, Sus scrofa; Gg, Gallus gallus; Xt, Xenopus tropicalis; Dr, Danio rerio; Sas, Salmo salar; Bf, Branchiostoma floridae; Ci, Ciona intestinalis; Dm, Drosophila melanogaster; Ce, Caenorhabditis elegans; Mb, Monosiga brevicollis. ADF/CFL family number is given next to species designation when available. For those sequences that did not have a published family number on NCBI, the accession number is given. Accession numbers for all animal ADF/CFL variants used in analyses can be found in S2 Table.
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pone.0145917.g002: Bayesian phylogenetic analysis of the animal ADF/CFL gene family.The three ADF/CFL classes are highlighted in boxes. Species designation are as follows: Hs, Homo sapiens; Mm, Mus musculus; Ss, Sus scrofa; Gg, Gallus gallus; Xt, Xenopus tropicalis; Dr, Danio rerio; Sas, Salmo salar; Bf, Branchiostoma floridae; Ci, Ciona intestinalis; Dm, Drosophila melanogaster; Ce, Caenorhabditis elegans; Mb, Monosiga brevicollis. ADF/CFL family number is given next to species designation when available. For those sequences that did not have a published family number on NCBI, the accession number is given. Accession numbers for all animal ADF/CFL variants used in analyses can be found in S2 Table.

Mentions: The phylogenetic analysis of the animal ADF/CFLs revealed that the invertebrate and vertebrate ADF/CFL sequences group separately from one another (Fig 2). It should be noted that the chordate species (C. intestinalis and B. floridae) did not form a monophyletic group in the phylogeny. The vertebrate ADF/CFL variants further diverge into three main classes: CFL1, CFL2, and ADF/Destrin. Of these, only mammals contained representatives in all three classes, and only in the mammalian lineage did we find the non-muscle CFL1 variants. All other vertebrate species had representatives only in the CFL2 and ADF/Destrin classes. Our phylogenetic analysis provided greater resolution for two particular lineages than has been previously published for the amphibian X. tropicalis and the two bony fish species, D. rerio and S. salar. As with mammals, fish possess three distinct ADF/CFL variants. However, only the S. salar and D. rerio CFL2 variant grouped within the other vertebrate ADF/CFL sequences, the muscle-specific CFL2 class. The remaining fish ADF/CFL variants grouped outside of the three vertebrate classes, possibly as a fourth class of ADF/CFL variants, suggesting that these protein variants have progressed on an independent evolutionary trajectory that is unique to fishes (Fig 2). The frog Xenopus tropicalis has two ADF/CFL variants that have historically been shown to group with each other, outside of the three conserved classes of vertebrate ADF/CFLs [8, 9]. In our analysis, the two X. tropicalis variants grouped within the vertebrate sequences, with one variant in the vertebrate ADF/Destrin group and the second variant in the muscle-specific CFL2 group (Fig 2).


Phylogenetic Patterns of Codon Evolution in the ACTIN-DEPOLYMERIZING FACTOR/COFILIN (ADF/CFL) Gene Family.

Roy-Zokan EM, Dyer KA, Meagher RB - PLoS ONE (2015)

Bayesian phylogenetic analysis of the animal ADF/CFL gene family.The three ADF/CFL classes are highlighted in boxes. Species designation are as follows: Hs, Homo sapiens; Mm, Mus musculus; Ss, Sus scrofa; Gg, Gallus gallus; Xt, Xenopus tropicalis; Dr, Danio rerio; Sas, Salmo salar; Bf, Branchiostoma floridae; Ci, Ciona intestinalis; Dm, Drosophila melanogaster; Ce, Caenorhabditis elegans; Mb, Monosiga brevicollis. ADF/CFL family number is given next to species designation when available. For those sequences that did not have a published family number on NCBI, the accession number is given. Accession numbers for all animal ADF/CFL variants used in analyses can be found in S2 Table.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4696841&req=5

pone.0145917.g002: Bayesian phylogenetic analysis of the animal ADF/CFL gene family.The three ADF/CFL classes are highlighted in boxes. Species designation are as follows: Hs, Homo sapiens; Mm, Mus musculus; Ss, Sus scrofa; Gg, Gallus gallus; Xt, Xenopus tropicalis; Dr, Danio rerio; Sas, Salmo salar; Bf, Branchiostoma floridae; Ci, Ciona intestinalis; Dm, Drosophila melanogaster; Ce, Caenorhabditis elegans; Mb, Monosiga brevicollis. ADF/CFL family number is given next to species designation when available. For those sequences that did not have a published family number on NCBI, the accession number is given. Accession numbers for all animal ADF/CFL variants used in analyses can be found in S2 Table.
Mentions: The phylogenetic analysis of the animal ADF/CFLs revealed that the invertebrate and vertebrate ADF/CFL sequences group separately from one another (Fig 2). It should be noted that the chordate species (C. intestinalis and B. floridae) did not form a monophyletic group in the phylogeny. The vertebrate ADF/CFL variants further diverge into three main classes: CFL1, CFL2, and ADF/Destrin. Of these, only mammals contained representatives in all three classes, and only in the mammalian lineage did we find the non-muscle CFL1 variants. All other vertebrate species had representatives only in the CFL2 and ADF/Destrin classes. Our phylogenetic analysis provided greater resolution for two particular lineages than has been previously published for the amphibian X. tropicalis and the two bony fish species, D. rerio and S. salar. As with mammals, fish possess three distinct ADF/CFL variants. However, only the S. salar and D. rerio CFL2 variant grouped within the other vertebrate ADF/CFL sequences, the muscle-specific CFL2 class. The remaining fish ADF/CFL variants grouped outside of the three vertebrate classes, possibly as a fourth class of ADF/CFL variants, suggesting that these protein variants have progressed on an independent evolutionary trajectory that is unique to fishes (Fig 2). The frog Xenopus tropicalis has two ADF/CFL variants that have historically been shown to group with each other, outside of the three conserved classes of vertebrate ADF/CFLs [8, 9]. In our analysis, the two X. tropicalis variants grouped within the vertebrate sequences, with one variant in the vertebrate ADF/Destrin group and the second variant in the muscle-specific CFL2 group (Fig 2).

Bottom Line: Estimating the rate of non-synonymous to synonymous mutations (dN/dS) across phylogenetic lineages revealed that the majority of ADF/CFL codon positions were under strong purifying selection, with rare episodic events of accelerated protein evolution.In both plants and animals these instances of accelerated evolution were ADF/CFL subclass specific, and all of the sites under selection were located in regions of the protein that could serve in new functional roles.We suggest these sites may have been important in the functional diversification of ADF/CFL proteins.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, University of Georgia, Athens, Georgia, United States of America.

ABSTRACT
The actin-depolymerizing factor/cofilin (ADF/CFL) gene family encodes a diverse group of relatively small proteins. Once known strictly as modulators of actin filament dynamics, recent research has demonstrated that these proteins are involved in a variety of cellular processes, from signal transduction to the cytonuclear trafficking of actin. In both plant and animal lineages, expression patterns of paralogs in the ADF/CFL gene family vary among tissue types and developmental stages. In this study we use computational approaches to investigate the evolutionary forces responsible for the diversification of the ADF/CFL gene family. Estimating the rate of non-synonymous to synonymous mutations (dN/dS) across phylogenetic lineages revealed that the majority of ADF/CFL codon positions were under strong purifying selection, with rare episodic events of accelerated protein evolution. In both plants and animals these instances of accelerated evolution were ADF/CFL subclass specific, and all of the sites under selection were located in regions of the protein that could serve in new functional roles. We suggest these sites may have been important in the functional diversification of ADF/CFL proteins.

Show MeSH
Related in: MedlinePlus