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Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies.

Fetterman CD, Rannala B, Walter MA - BMC Evol. Biol. (2008)

Bottom Line: Branch-site models, which allow estimated selection pressures along specified lineages to vary as compared to the remaining phylogeny, identified positive selection along branches leading to the FoxA3 and Protostomia clades in the FoxA cluster and the branch leading to the FoxO3 clade in the FoxO cluster.Consideration of selection pressures observed in conjunction with known functional information allowed prediction of residue function and refinement of domain boundaries.Identification of residues that differentiate orthologs and paralogs provided insight into the development and functional consequences of paralogs and forkhead subfamily composition differences among species.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada. christina.fetterman@ualberta.ca

ABSTRACT

Background: Members of the forkhead gene family act as transcription regulators in biological processes including development and metabolism. The evolution of forkhead genes has not been widely examined and selection pressures at the molecular level influencing subfamily evolution and differentiation have not been explored. Here, in silico methods were used to examine selection pressures acting on the coding sequence of five multi-species FOX protein subfamily clusters; FoxA, FoxD, FoxI, FoxO and FoxP.

Results: Application of site models, which estimate overall selection pressures on individual codons throughout the phylogeny, showed that the amino acid changes observed were either neutral or under negative selection. Branch-site models, which allow estimated selection pressures along specified lineages to vary as compared to the remaining phylogeny, identified positive selection along branches leading to the FoxA3 and Protostomia clades in the FoxA cluster and the branch leading to the FoxO3 clade in the FoxO cluster. Residues that may differentiate paralogs were identified in the FoxA and FoxO clusters and residues that differentiate orthologs were identified in the FoxA cluster. Neutral amino acid changes were identified in the forkhead domain of the FoxA, FoxD and FoxP clusters while positive selection was identified in the forkhead domain of the Protostomia lineage of the FoxA cluster. A series of residues under strong negative selection adjacent to the N- and C-termini of the forkhead domain were identified in all clusters analyzed suggesting a new method for refinement of domain boundaries. Extrapolation of domains among cluster members in conjunction with selection pressure information allowed prediction of residue function in the FoxA, FoxO and FoxP clusters and exclusion of known domain function in residues of the FoxA and FoxI clusters.

Conclusion: Consideration of selection pressures observed in conjunction with known functional information allowed prediction of residue function and refinement of domain boundaries. Identification of residues that differentiate orthologs and paralogs provided insight into the development and functional consequences of paralogs and forkhead subfamily composition differences among species. Overall we found that after gene duplication of forkhead family members, rapid differentiation and subsequent fixation of amino acid changes through negative selection has occurred.

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Residues experiencing neutral changes and positive selection in the forkhead domain. The forkhead domain of FOXA3 is shown bound to DNA. Residues with neutral changes identified in the FoxA (blue), FoxD (red) and FoxP (yellow) clusters and residues under positive selection identified in the Protostomia lineage of the FoxA cluster (orange) are highlighted and indicated with arrows. Alpha helices 1, 2 and 3, beta sheets 1 and 2, and wings 1 and 2 are denoted H1, H2, H3, B1, B2, W1 and W2 respectively.
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Figure 3: Residues experiencing neutral changes and positive selection in the forkhead domain. The forkhead domain of FOXA3 is shown bound to DNA. Residues with neutral changes identified in the FoxA (blue), FoxD (red) and FoxP (yellow) clusters and residues under positive selection identified in the Protostomia lineage of the FoxA cluster (orange) are highlighted and indicated with arrows. Alpha helices 1, 2 and 3, beta sheets 1 and 2, and wings 1 and 2 are denoted H1, H2, H3, B1, B2, W1 and W2 respectively.

Mentions: In the FoxA cluster Protostomia lineage a number of residues under positive selection were found in the forkhead domain through branch-site analysis. These residues are located within helix 2, β-sheet 2 and wing 1 as defined by the crystal structure of FoxA3 [63] (Figure 3, see Additional file 3(A)). The residues corresponding to the positively selected sites in the Protostomia lineage are 100 percent conserved among the other sequences analyzed. It is possible that these changes in amino acid composition of the forkhead domain alter the domain configuration thus allowing for different target binding and/or regulation of FoxA genes in the Protostomia as compared to the Deuterostomia. It is interesting to note that to date, in most Protostomia only one FoxA class gene has been identified while in the Deuterostomia, multiple FoxA class genes have been found. If FoxA targets are similar in the Protostomia and Deuterostomia lineages, the alterations in the forkhead domain of Protostomia FoxA may allow these single proteins to perform the same function that require multiple FoxA proteins in the Deuterostomia. This theory is further supported by the differences observed in the N-terminal region of the Protostomia FoxA and in conserved domain III as compared to the Deuterostomia discussed earlier.


Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies.

Fetterman CD, Rannala B, Walter MA - BMC Evol. Biol. (2008)

Residues experiencing neutral changes and positive selection in the forkhead domain. The forkhead domain of FOXA3 is shown bound to DNA. Residues with neutral changes identified in the FoxA (blue), FoxD (red) and FoxP (yellow) clusters and residues under positive selection identified in the Protostomia lineage of the FoxA cluster (orange) are highlighted and indicated with arrows. Alpha helices 1, 2 and 3, beta sheets 1 and 2, and wings 1 and 2 are denoted H1, H2, H3, B1, B2, W1 and W2 respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2570691&req=5

Figure 3: Residues experiencing neutral changes and positive selection in the forkhead domain. The forkhead domain of FOXA3 is shown bound to DNA. Residues with neutral changes identified in the FoxA (blue), FoxD (red) and FoxP (yellow) clusters and residues under positive selection identified in the Protostomia lineage of the FoxA cluster (orange) are highlighted and indicated with arrows. Alpha helices 1, 2 and 3, beta sheets 1 and 2, and wings 1 and 2 are denoted H1, H2, H3, B1, B2, W1 and W2 respectively.
Mentions: In the FoxA cluster Protostomia lineage a number of residues under positive selection were found in the forkhead domain through branch-site analysis. These residues are located within helix 2, β-sheet 2 and wing 1 as defined by the crystal structure of FoxA3 [63] (Figure 3, see Additional file 3(A)). The residues corresponding to the positively selected sites in the Protostomia lineage are 100 percent conserved among the other sequences analyzed. It is possible that these changes in amino acid composition of the forkhead domain alter the domain configuration thus allowing for different target binding and/or regulation of FoxA genes in the Protostomia as compared to the Deuterostomia. It is interesting to note that to date, in most Protostomia only one FoxA class gene has been identified while in the Deuterostomia, multiple FoxA class genes have been found. If FoxA targets are similar in the Protostomia and Deuterostomia lineages, the alterations in the forkhead domain of Protostomia FoxA may allow these single proteins to perform the same function that require multiple FoxA proteins in the Deuterostomia. This theory is further supported by the differences observed in the N-terminal region of the Protostomia FoxA and in conserved domain III as compared to the Deuterostomia discussed earlier.

Bottom Line: Branch-site models, which allow estimated selection pressures along specified lineages to vary as compared to the remaining phylogeny, identified positive selection along branches leading to the FoxA3 and Protostomia clades in the FoxA cluster and the branch leading to the FoxO3 clade in the FoxO cluster.Consideration of selection pressures observed in conjunction with known functional information allowed prediction of residue function and refinement of domain boundaries.Identification of residues that differentiate orthologs and paralogs provided insight into the development and functional consequences of paralogs and forkhead subfamily composition differences among species.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada. christina.fetterman@ualberta.ca

ABSTRACT

Background: Members of the forkhead gene family act as transcription regulators in biological processes including development and metabolism. The evolution of forkhead genes has not been widely examined and selection pressures at the molecular level influencing subfamily evolution and differentiation have not been explored. Here, in silico methods were used to examine selection pressures acting on the coding sequence of five multi-species FOX protein subfamily clusters; FoxA, FoxD, FoxI, FoxO and FoxP.

Results: Application of site models, which estimate overall selection pressures on individual codons throughout the phylogeny, showed that the amino acid changes observed were either neutral or under negative selection. Branch-site models, which allow estimated selection pressures along specified lineages to vary as compared to the remaining phylogeny, identified positive selection along branches leading to the FoxA3 and Protostomia clades in the FoxA cluster and the branch leading to the FoxO3 clade in the FoxO cluster. Residues that may differentiate paralogs were identified in the FoxA and FoxO clusters and residues that differentiate orthologs were identified in the FoxA cluster. Neutral amino acid changes were identified in the forkhead domain of the FoxA, FoxD and FoxP clusters while positive selection was identified in the forkhead domain of the Protostomia lineage of the FoxA cluster. A series of residues under strong negative selection adjacent to the N- and C-termini of the forkhead domain were identified in all clusters analyzed suggesting a new method for refinement of domain boundaries. Extrapolation of domains among cluster members in conjunction with selection pressure information allowed prediction of residue function in the FoxA, FoxO and FoxP clusters and exclusion of known domain function in residues of the FoxA and FoxI clusters.

Conclusion: Consideration of selection pressures observed in conjunction with known functional information allowed prediction of residue function and refinement of domain boundaries. Identification of residues that differentiate orthologs and paralogs provided insight into the development and functional consequences of paralogs and forkhead subfamily composition differences among species. Overall we found that after gene duplication of forkhead family members, rapid differentiation and subsequent fixation of amino acid changes through negative selection has occurred.

Show MeSH