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FoxO gene family evolution in vertebrates.

Wang M, Zhang X, Zhao H, Wang Q, Pan Y - BMC Evol. Biol. (2009)

Bottom Line: Our results suggest that FoxO is constrained by strong purifying selection except four sites in FoxO6, which have undergone positive Darwinian selection.The functional divergence in this family is best explained by either relaxed purifying selection or positive selection.Relaxed selection may play important roles in the process of functional differentiation evolved through gene duplications as well.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Agriculture and Biology, Department of Animal Sciences, Shanghai Jiao Tong University, Shanghai, 200240, PR China. wangmh-1981@sjtu.edu.cn

ABSTRACT

Background: Forkhead box, class O (FoxO) belongs to the large family of forkhead transcription factors that are characterized by a conserved forkhead box DNA-binding domain. To date, the FoxO group has four mammalian members: FoxO1, FoxO3a, FoxO4 and FoxO6, which are orthologs of DAF16, an insulin-responsive transcription factor involved in regulating longevity of worms and flies. The degree of homology between these four members is high, especially in the forkhead domain, which contains the DNA-binding interface. Yet, mouse FoxO knockouts have revealed that each FoxO gene has its unique role in the physiological process. Whether the functional divergences are primarily due to adaptive selection pressure or relaxed selective constraint remains an open question. As such, this study aims to address the evolutionary mode of FoxO, which may lead to the functional divergence.

Results: Sequence similarity searches have performed in genome and scaffold data to identify homologues of FoxO in vertebrates. Phylogenetic analysis was used to characterize the family evolutionary history by identifying two duplications early in vertebrate evolution. To determine the mode of evolution in vertebrates, we performed a rigorous statistical analysis with FoxO gene sequences, including relative rate ratio tests, branch-specific dN/dS ratio tests, site-specific dN/dS ratio tests, branch-site dN/dS ratio tests and clade level amino acid conservation/variation patterns analysis. Our results suggest that FoxO is constrained by strong purifying selection except four sites in FoxO6, which have undergone positive Darwinian selection. The functional divergence in this family is best explained by either relaxed purifying selection or positive selection.

Conclusion: We present a phylogeny describing the evolutionary history of the FoxO gene family and show that the genes have evolved through duplications followed by purifying selection except for four sites in FoxO6 fixed by positive selection lie mostly within the non-conserved optimal PKB motif in the C-terminal part. Relaxed selection may play important roles in the process of functional differentiation evolved through gene duplications as well.

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The modeled structure of mouse Foxo6. A. The structure of the forkhead domain; B. Sequence logo of the forkhead domain and surrounding amino acids.
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Figure 4: The modeled structure of mouse Foxo6. A. The structure of the forkhead domain; B. Sequence logo of the forkhead domain and surrounding amino acids.

Mentions: Because of the evidence for possible positive selection on FoxO6, we predicted positively selected codon sites using a Bayes empirical Bayes (BEB) method [45]. The sites under selection in FoxO6 are listed in Table 5. Four codon sites were identified as positively selected at a BEB posterior probability threshold of 95%. Moreover, 7 amino acid residues presumably submitted to altered functional constraints were identified by both PAML 4 and Diverge 2.0 analysis (Table 6). In order to plot positive selected sites onto mouse (Foxo6) three-dimensional model, we first built an energy-minimized model using a homology modeling approach [60]. The PDB entry with the highest sequence similarity -identified in the PSI-BLAST- corresponds to the human FOXO3A (PDB: 2k86). We used this entry as a template for the modelling. The in silico stereochemical quality analysis [61] indicated that the generated model had a moderate quality (with the percentage of residues in most favored regions being no lower than the 82.8%), with only 1.1% in disallowed regions. As expected, the modeled structure was roughly similar to the template, with the three helices and two wing loops typical of the Fox family in equivalent positions and with a similar predicted folding (Figure 4). Taken together, these data suggested that the model was stereochemically valid, and therefore suitable for further sequence-structural analysis. Unfortunately, we could not map any positive selected sites onto the surface of the 3D structure (Figure 4A) because the crystal structures about Fox proteins are mainly focused on the forkhead DNA-binding domain. Whereas the positive selected sites were mainly located in the region of N-terminal and C-terminal of FoxO6, which also indicated that FoxO6 underwent strong constraint on the forkhead domain as well (Sequence logo of the forkhead domain, Figure 4).


FoxO gene family evolution in vertebrates.

Wang M, Zhang X, Zhao H, Wang Q, Pan Y - BMC Evol. Biol. (2009)

The modeled structure of mouse Foxo6. A. The structure of the forkhead domain; B. Sequence logo of the forkhead domain and surrounding amino acids.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2746812&req=5

Figure 4: The modeled structure of mouse Foxo6. A. The structure of the forkhead domain; B. Sequence logo of the forkhead domain and surrounding amino acids.
Mentions: Because of the evidence for possible positive selection on FoxO6, we predicted positively selected codon sites using a Bayes empirical Bayes (BEB) method [45]. The sites under selection in FoxO6 are listed in Table 5. Four codon sites were identified as positively selected at a BEB posterior probability threshold of 95%. Moreover, 7 amino acid residues presumably submitted to altered functional constraints were identified by both PAML 4 and Diverge 2.0 analysis (Table 6). In order to plot positive selected sites onto mouse (Foxo6) three-dimensional model, we first built an energy-minimized model using a homology modeling approach [60]. The PDB entry with the highest sequence similarity -identified in the PSI-BLAST- corresponds to the human FOXO3A (PDB: 2k86). We used this entry as a template for the modelling. The in silico stereochemical quality analysis [61] indicated that the generated model had a moderate quality (with the percentage of residues in most favored regions being no lower than the 82.8%), with only 1.1% in disallowed regions. As expected, the modeled structure was roughly similar to the template, with the three helices and two wing loops typical of the Fox family in equivalent positions and with a similar predicted folding (Figure 4). Taken together, these data suggested that the model was stereochemically valid, and therefore suitable for further sequence-structural analysis. Unfortunately, we could not map any positive selected sites onto the surface of the 3D structure (Figure 4A) because the crystal structures about Fox proteins are mainly focused on the forkhead DNA-binding domain. Whereas the positive selected sites were mainly located in the region of N-terminal and C-terminal of FoxO6, which also indicated that FoxO6 underwent strong constraint on the forkhead domain as well (Sequence logo of the forkhead domain, Figure 4).

Bottom Line: Our results suggest that FoxO is constrained by strong purifying selection except four sites in FoxO6, which have undergone positive Darwinian selection.The functional divergence in this family is best explained by either relaxed purifying selection or positive selection.Relaxed selection may play important roles in the process of functional differentiation evolved through gene duplications as well.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Agriculture and Biology, Department of Animal Sciences, Shanghai Jiao Tong University, Shanghai, 200240, PR China. wangmh-1981@sjtu.edu.cn

ABSTRACT

Background: Forkhead box, class O (FoxO) belongs to the large family of forkhead transcription factors that are characterized by a conserved forkhead box DNA-binding domain. To date, the FoxO group has four mammalian members: FoxO1, FoxO3a, FoxO4 and FoxO6, which are orthologs of DAF16, an insulin-responsive transcription factor involved in regulating longevity of worms and flies. The degree of homology between these four members is high, especially in the forkhead domain, which contains the DNA-binding interface. Yet, mouse FoxO knockouts have revealed that each FoxO gene has its unique role in the physiological process. Whether the functional divergences are primarily due to adaptive selection pressure or relaxed selective constraint remains an open question. As such, this study aims to address the evolutionary mode of FoxO, which may lead to the functional divergence.

Results: Sequence similarity searches have performed in genome and scaffold data to identify homologues of FoxO in vertebrates. Phylogenetic analysis was used to characterize the family evolutionary history by identifying two duplications early in vertebrate evolution. To determine the mode of evolution in vertebrates, we performed a rigorous statistical analysis with FoxO gene sequences, including relative rate ratio tests, branch-specific dN/dS ratio tests, site-specific dN/dS ratio tests, branch-site dN/dS ratio tests and clade level amino acid conservation/variation patterns analysis. Our results suggest that FoxO is constrained by strong purifying selection except four sites in FoxO6, which have undergone positive Darwinian selection. The functional divergence in this family is best explained by either relaxed purifying selection or positive selection.

Conclusion: We present a phylogeny describing the evolutionary history of the FoxO gene family and show that the genes have evolved through duplications followed by purifying selection except for four sites in FoxO6 fixed by positive selection lie mostly within the non-conserved optimal PKB motif in the C-terminal part. Relaxed selection may play important roles in the process of functional differentiation evolved through gene duplications as well.

Show MeSH