The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint
The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint
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DOI：
10.1101/gr.2195604
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发表时间：
2004-05-01
期刊：
影响因子：
7
通讯作者：
Kulathinal, RJ
中科院分区：
文献类型：
--
作者：
Castillo-Davis, CI;Kondrashov, FA;Kulathinal, RJ
我们比较了两个不同动物谱系中蛋白质进化的功能谱，并提出了两个假设：（1）在两个谱系中，蛋白质组的分化率在功能类别中的分布相似，表明蛋白质组的选择压力在很大程度上与生物体水平的生物学要求无关;和（2）分歧率分布在不同的功能类在每个血统，表明物种特异性的选择制度影响全基因组的替代模式。将比较基因组序列与来自组织特异性表达序列标签（EST）文库和详细的数据库注释的数据相结合，我们发现哺乳动物和线虫谱系之间共享的快速进化和选择性约束的功能基因组签名，尽管它们具有广泛的形态和生态差异以及遥远的共同祖先。在这两个门，我们发现的证据加速进化的分子系统的组成部分参与共同进化的变化。在哺乳动物中，谱系特异性快速进化的基因包括那些涉及生殖，免疫，可能，母胎冲突。似然比检验为哺乳动物中这些快速进化的功能类别的正选择提供了证据。相比之下，在两个门中缓慢进化的基因，在氨基酸或插入/缺失（indel）变化方面，参与核心分子过程，如转录，翻译和蛋白质转运。因此，强大的纯化选择似乎作用于哺乳动物和线虫谱系中相同的核心细胞过程，而积极和/或放松的选择作用于每个谱系中不同的生物过程。
We compare the functional spectrum of protein evolution in two separate animal lineages with respect to two hypotheses: (1) rates of divergence are distributed similarly among functional classes within both lineages, indicating that selective pressure on the proteome is largely independent of organismic-level biological requirements; and (2) rates of divergence are distributed differently among functional classes within each lineage, indicating species-specific selective regimes impact genome-wide substitutional patterns. Integrating comparative genome sequence with data from tissue-specific expressed-sequence-tag (EST) libraries and detailed database annotations, we find a functional genomic signature of rapid evolution and selective constraint shared between mammalian and nematode lineages despite their extensive morphological and ecological differences and distant common ancestry. In both phyla, we find evidence of accelerated evolution among components of molecular systems involved in coevolutionary change. In mammals, lineage-specific fast evolving genes include those involved in reproduction, immunity, and possibly, maternal-fetal conflict. Likelihood ratio tests provide evidence for positive selection in these rapidly evolving functional categories in mammals. In contrast, slowly evolving genes, in terms of amino acid or insertion/deletion (indel) change, in both phyla are involved in core molecular processes such as transcription, translation, and protein transport. Thus, strong purifying selection appears to act on the same core cellular processes in both mammalian and nematode lineages, whereas positive and/or relaxed selection acts on different biological processes in each lineage.