Wang Minghui, Zhang Xiangzhe, Zhao Hongbo, Wang Qishan, Pan Yuchun
School of Agriculture and Biology, Department of Animal Sciences, Shanghai Jiao Tong University, Shanghai, 200240, PR China.
BMC Evol Biol. 2009 Sep 7;9:222. doi: 10.1186/1471-2148-9-222.
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.
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.
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.
叉头框O类（FoxO）属于叉头转录因子大家族，其特征是具有保守的叉头框DNA结合结构域。迄今为止，FoxO家族在哺乳动物中有四个成员：FoxO1、FoxO3a、FoxO4和FoxO6，它们是DAF16的直系同源物，DAF16是一种参与调节蠕虫和果蝇寿命的胰岛素反应性转录因子。这四个成员之间的同源程度很高，尤其是在包含DNA结合界面的叉头结构域。然而，小鼠FoxO基因敲除实验表明，每个FoxO基因在生理过程中都有其独特的作用。功能差异主要是由于适应性选择压力还是放松的选择约束，仍然是一个悬而未决的问题。因此，本研究旨在探讨FoxO的进化模式，这可能导致其功能差异。
在基因组和支架数据中进行了序列相似性搜索，以鉴定脊椎动物中FoxO的同源物。系统发育分析用于通过识别脊椎动物进化早期的两次复制来表征该家族的进化历史。为了确定脊椎动物中的进化模式，我们对FoxO基因序列进行了严格的统计分析，包括相对速率比测试、分支特异性dN/dS比率测试、位点特异性dN/dS比率测试、分支-位点dN/dS比率测试以及进化枝水平的氨基酸保守/变异模式分析。我们的结果表明，除了FoxO6中的四个位点经历了正达尔文选择外，FoxO受到强烈的纯化选择的限制。这个家族中的功能差异最好用放松的纯化选择或正选择来解释。
我们展示了一个描述FoxO基因家族进化历史的系统发育树，并表明这些基因通过复制进化，随后进行纯化选择，但FoxO6中的四个位点通过正选择固定，这些位点大多位于C端非保守的最佳PKB基序内。放松选择在通过基因复制进化的功能分化过程中也可能起重要作用。
