Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes
Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes
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DOI：
10.1093/nar/gkh815
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发表时间：
2004-01-01
影响因子：
14.9
通讯作者：
Huynen, MA
中科院分区：
文献类型：
--
作者：
Snel, B;van Noort, V;Huynen, MA
物种之间的差异主要存在于基因之间的连接网络中。然而，这些联系的发展速度还没有得到适当的量化。在这里，我们测量了基因对之间的共同调节在大系统发育距离上的保守程度；在两种真核生物秀丽隐杆线虫和酿酒酵母之间，在两种原核生物大肠杆菌和枯草芽孢杆菌之间。我们首先结合酵母的各种功能基因组学数据构建了一组可靠的共调控基因，随后从共表达值的分布确定了蠕虫中共调控的保守性。对于枯草芽孢杆菌和大肠杆菌，我们使用已知的操纵子和调控子。我们发现76%到80%的共调控连接在同源基因对之间是保守的，这与之前对网络进化的估计和期望相比是非常高的。我们表明，在物种形成后基因复制的情况下，两个非同源基因中的一个倾向于保留其原始的共同调节关系，而另一个失去这种联系，可能是自由分化或亚功能化。高水平的共调控守恒意味着，当一个物种也拥有相关基因时，从功能基因组学数据中可靠预测的功能关系可以高精度地转移到另一个物种。
Differences between species have been suggested to largely reside in the network of connections among the genes. Nevertheless, the rate at which these connections evolve has not been properly quantified. Here, we measure the extent to which co-regulation between pairs of genes is conserved over large phylogenetic distances; between two eukaryotes Caenorhabditis elegans and Saccharomyces cerevisiae, and between two prokaryotes Escherichia coli and Bacillus subtilis. We first construct a reliable set of co-regulated genes by combining various functional genomics data from yeast, and subsequently determine conservation of co-regulation in worm from the distribution of co-expression values. For B.subtilis and E.coli, we use known operons and regulons. We find that between 76 and 80% of the co-regulatory connections are conserved between orthologous pairs of genes, which is very high compared with previous estimates and expectations regarding network evolution. We show that in the case of gene duplication after speciation, one of the two inparalogous genes tends to retain its original co-regulatory relationship, while the other loses this link and is presumably free for differentiation or sub-functionalization. The high level of co-regulation conservation implies that reliably predicted functional relationships from functional genomics data in one species can be transferred with high accuracy to another species when that species also harbours the associated genes.