The evolution of human cells in terms of protein innovation.
The evolution of human cells in terms of protein innovation.
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DOI：
10.1093/molbev/mst139
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发表时间：
2014-06
影响因子：
10.7
通讯作者：
Rackham OJ
中科院分区：
文献类型：
--
作者：
Sardar AJ;Oates ME;Fang H;Forrest AR;Kawaji H;FANTOM Consortium;Gough J;Rackham OJ
人类由数百种细胞类型组成。由于每个体细胞的基因组DNA是相同的，细胞类型由表达的内容和时间决定。直到最近，关于人类细胞特性的决定因素的报道很少，特别是从基因进化和表达的联合角度。在这里，我们通过基因表达的主要产物蛋白质的集体历史，绘制出所有已记录的人类细胞类型的进化历史。FANTOM5数据提供特定细胞类型的人类蛋白质编码基因的数字表达，超家族资源用于提供蛋白质结构域注释。每种蛋白质产生的进化时代是通过与所有其他完全测序的基因组的结构域注释进行比较来推断的。研究在每种细胞类型中表达的基因的跨时代分布，可以从蛋白质创新的角度洞察人类细胞的进化。对于每一种细胞类型，它的蛋白质创新历史都是基于它所表达的基因绘制的。结合所有细胞类型的历史使我们能够创建细胞进化的时间线。这一时间线确定了这样一种可能性，即我们共同的祖先腔体动物(形成洞穴的动物)提供了先天性免疫系统所需的创新，而现在构成人类大脑的细胞自Opisthokonta(动物和真菌的边界)以来一直遵循着不断积累新蛋白质的轨迹。我们得出的结论是，将现有的域体系结构扩展到新的上下文中是特定于单元类型的域体系结构的主要来源。
Humans are composed of hundreds of cell types. As the genomic DNA of each somatic cell is identical, cell type is determined by what is expressed and when. Until recently, little has been reported about the determinants of human cell identity, particularly from the joint perspective of gene evolution and expression. Here, we chart the evolutionary past of all documented human cell types via the collective histories of proteins, the principal product of gene expression. FANTOM5 data provide cell-type–specific digital expression of human protein-coding genes and the SUPERFAMILY resource is used to provide protein domain annotation. The evolutionary epoch in which each protein was created is inferred by comparison with domain annotation of all other completely sequenced genomes. Studying the distribution across epochs of genes expressed in each cell type reveals insights into human cellular evolution in terms of protein innovation. For each cell type, its history of protein innovation is charted based on the genes it expresses. Combining the histories of all cell types enables us to create a timeline of cell evolution. This timeline identifies the possibility that our common ancestor Coelomata (cavity-forming animals) provided the innovation required for the innate immune system, whereas cells which now form the brain of human have followed a trajectory of continually accumulating novel proteins since Opisthokonta (boundary of animals and fungi). We conclude that exaptation of existing domain architectures into new contexts is the dominant source of cell-type–specific domain architectures.
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