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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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Codon positions with highest probability of being in the ω3 rate category within plant and animal phylogenies.The codon positions (A) 157 (B) 26 and (C) 9 were found to be in the ω3 rate category in the plant ADF phylogeny. The codon positions (D) 125 and (E) 69 were found in the ω3 rate category in the animal ADF/CFL phylogeny. Red branches have the highest probability of being in the ω3 rate category, gray branches represents branches with the highest probability in the ω2 rate category, and blue branches represents branches with the highest probability of being in the ω1 rate category.
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pone.0145917.g004: Codon positions with highest probability of being in the ω3 rate category within plant and animal phylogenies.The codon positions (A) 157 (B) 26 and (C) 9 were found to be in the ω3 rate category in the plant ADF phylogeny. The codon positions (D) 125 and (E) 69 were found in the ω3 rate category in the animal ADF/CFL phylogeny. Red branches have the highest probability of being in the ω3 rate category, gray branches represents branches with the highest probability in the ω2 rate category, and blue branches represents branches with the highest probability of being in the ω1 rate category.

Mentions: To discern where along the ADF/CFL protein sequence these sites occurred, the number of branches within the phylogeny that had the highest probability of containing a particular amino acid position within the ω3 rate category (i.e., the highest rate of dN/dS) was plotted across the linear protein sequence (Fig 3A and 3B). All codon positions are based on the protein alignments used for the phylogenetic analysis and selection analyses. In the plant ADF gene family, 10 of the 11 amino acid positions with highest probability of being grouped within the ω3 rate class were located outside of any known G-actin and F-actin binding domains and were also not within the nuclear localization sequence (NLS) (Fig 3A). Two of the sites, codon positions 9 and 157, had a relatively large number of branches in the ω3 rate class. Plotting these branches on the phylogeny identified subclass specific as well as monocot and dicot specific patterns of relaxed purifying selection (Fig 4A–4C). Codon position 9 is located in the N-terminal tail of the ADF protein and was found to have the highest probability of being in the ω3 rate category for dicot ADF variants within subclass IV only (Fig 4C). Likewise, codon position 157 is located in the C-terminal tail of the ADF protein and was found to be in the ω3 rate category for Subclass II dicot ADF variants only (Fig 4A). Additionally, codon position 26 was found to have experienced accelerated rates of evolution in the subclass III monocot ADF variants (Fig 4B). Mapping codon position 26 onto a 3D model of Z. mays ADF5, a subclass III monocot ADF variant, showed that this particular site is located on an alpha helix that lies on the exterior of the protein with its side chain exposed (Fig 5A).


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)

Codon positions with highest probability of being in the ω3 rate category within plant and animal phylogenies.The codon positions (A) 157 (B) 26 and (C) 9 were found to be in the ω3 rate category in the plant ADF phylogeny. The codon positions (D) 125 and (E) 69 were found in the ω3 rate category in the animal ADF/CFL phylogeny. Red branches have the highest probability of being in the ω3 rate category, gray branches represents branches with the highest probability in the ω2 rate category, and blue branches represents branches with the highest probability of being in the ω1 rate category.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0145917.g004: Codon positions with highest probability of being in the ω3 rate category within plant and animal phylogenies.The codon positions (A) 157 (B) 26 and (C) 9 were found to be in the ω3 rate category in the plant ADF phylogeny. The codon positions (D) 125 and (E) 69 were found in the ω3 rate category in the animal ADF/CFL phylogeny. Red branches have the highest probability of being in the ω3 rate category, gray branches represents branches with the highest probability in the ω2 rate category, and blue branches represents branches with the highest probability of being in the ω1 rate category.
Mentions: To discern where along the ADF/CFL protein sequence these sites occurred, the number of branches within the phylogeny that had the highest probability of containing a particular amino acid position within the ω3 rate category (i.e., the highest rate of dN/dS) was plotted across the linear protein sequence (Fig 3A and 3B). All codon positions are based on the protein alignments used for the phylogenetic analysis and selection analyses. In the plant ADF gene family, 10 of the 11 amino acid positions with highest probability of being grouped within the ω3 rate class were located outside of any known G-actin and F-actin binding domains and were also not within the nuclear localization sequence (NLS) (Fig 3A). Two of the sites, codon positions 9 and 157, had a relatively large number of branches in the ω3 rate class. Plotting these branches on the phylogeny identified subclass specific as well as monocot and dicot specific patterns of relaxed purifying selection (Fig 4A–4C). Codon position 9 is located in the N-terminal tail of the ADF protein and was found to have the highest probability of being in the ω3 rate category for dicot ADF variants within subclass IV only (Fig 4C). Likewise, codon position 157 is located in the C-terminal tail of the ADF protein and was found to be in the ω3 rate category for Subclass II dicot ADF variants only (Fig 4A). Additionally, codon position 26 was found to have experienced accelerated rates of evolution in the subclass III monocot ADF variants (Fig 4B). Mapping codon position 26 onto a 3D model of Z. mays ADF5, a subclass III monocot ADF variant, showed that this particular site is located on an alpha helix that lies on the exterior of the protein with its side chain exposed (Fig 5A).

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