General trends in the utilization of structural factors contributing to biological complexity.
General trends in the utilization of structural factors contributing to biological complexity.
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DOI：
10.1093/molbev/mss064
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发表时间：
2012-08
影响因子：
10.7
通讯作者：
Dong Yang;F. Zhong;Dong Li;Zhongyang Liu;Handong Wei;Ying Jiang;F. He
中科院分区：
文献类型：
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作者：
Dong Yang;F. Zhong;Dong Li;Zhongyang Liu;Handong Wei;Ying Jiang;F. He
在进化过程中，包含新出现的结构域的蛋白质和全基因组编码的蛋白质组（GEP）中多结构域蛋白质的比例增加，大大增加了生物的复杂性。然而，目前还不知道这两个潜在的结构因素是如何优先利用在给定的生理状态。在这里，我们根据结构域数量和结构域年龄对蛋白质进行分类，并探索了从GEP到各种特定状态蛋白质组（CSP，即，在某些生理状态下表达的所有蛋白质）。我们发现，与GEP相比，多结构域蛋白质或仅含较老结构域的蛋白质在CSP中显著过多，这是一种在多细胞生物中比单细胞生物更强的趋势。有趣的是，在多细胞真核生物的进化过程中，过度表达的强度下降了。当跨CSP进行比较时，我们发现多结构域蛋白在复杂组织中比在简单组织中更过度表达，而复杂组织和简单组织之间具有不同年龄结构域的蛋白质之间没有明显差异。因此，在某些条件下，生物的复杂性更显着地实现了不同的域组织比新类型的域的出现。此外，我们发现，多结构域或只有旧的结构域含有蛋白质往往演变缓慢，一般是在较强的纯化选择，这可能部分是由于他们的一般过度的CSP的趋势。
During evolution, proteins containing newly emerged domains and the increasing proportion of multidomain proteins in the full genome-encoded proteome (GEP) have substantially contributed to increasing biological complexity. However, it is not known how these two potential structural factors are preferentially utilized at given physiological states. Here, we classified proteins according to domain number and domain age and explored the general trends across species for the utilization of proteins from GEP to various certain-state proteomes (CSPs, i.e., all the proteins expressed at certain physiological states). We found that multidomain proteins or only older domain-containing proteins are significantly overrepresented in CSPs compared with GEP, which is a trend that is stronger in multicellular organisms than in unicellular organisms. Interestingly, the strengths of overrepresentation decreased during evolution of multicellular eukaryotes. When comparing across CSPs, we found that multidomain proteins are more overrepresented in complex tissues than in simpler ones, whereas no difference among proteins with domains of different ages is evident between complex and simple tissues. Thus, biological complexity under certain conditions is more significantly realized by diverse domain organization than by the emergence of new types of domain. In addition, we found that multidomain or only older domain-containing proteins tend to evolve slowly and generally are under stronger purifying selection, which may partly result from their general overrepresentation trends in CSPs.