Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana.
Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana.
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DOI：
10.1093/molbev/msq204
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发表时间：
2011-01
影响因子：
10.7
通讯作者：
Hirai MY
中科院分区：
文献类型：
--
作者：
Hanada K;Sawada Y;Kuromori T;Klausnitzer R;Saito K;Toyoda T;Shinozaki K;Li WH;Hirai MY
众所周知，在生物体中敲除一个基因往往不会产生表型效应。一种可能的解释是存在重复基因；也就是说，敲除一个基因的影响可由一个重复拷贝来补偿。另一种解释是存在替代途径。就代谢产物而言，这两种机制的相对作用在酵母中已被广泛研究，但在任何多细胞生物中尚未开展。在此，为了研究重复基因对代谢产物的功能补偿，我们通过高通量液相色谱 - 质谱（LC - MS）分析对拟南芥敲除突变体中1976个基因的35种代谢产物进行了定量。我们发现，在基因组中敲除单拷贝基因或具有远同源基因的重复基因往往比敲除具有近同源基因的重复基因引发更强的代谢效应，这表明只有具有近同源基因的重复基因在拟南芥代谢产物的功能补偿中起重要作用。为了扩展分析，我们检测了代谢网络中连通性高或低的代谢产物。我们发现当代谢物具有高连通性时，重复基因的补偿作用不太重要，这表明在高连通性的情况下，替代途径的功能补偿是常见的。总之，只有当替代途径数量较少时，近期复制的基因才在代谢产物的补偿中起重要作用。
It is well known that knocking out a gene in an organism often causes no phenotypic effect. One possible explanation is the existence of duplicate genes; that is, the effect of knocking out a gene is compensated by a duplicate copy. Another explanation is the existence of alternative pathways. In terms of metabolic products, the relative roles of the two mechanisms have been extensively studied in yeast but not in any multi-cellular organisms. Here, to address the functional compensation of metabolic products by duplicate genes, we quantified 35 metabolic products from 1,976 genes in knockout mutants of Arabidopsis thaliana by a high-throughput Liquid chromatography-Mass spectrometer (LC-MS) analysis. We found that knocking out either a singleton gene or a duplicate gene with distant paralogs in the genome tends to induce stronger metabolic effects than knocking out a duplicate gene with a close paralog in the genome, indicating that only duplicate genes with close paralogs play a significant role in functional compensation for metabolic products in A. thaliana. To extend the analysis, we examined metabolic products with either high or low connectivity in a metabolic network. We found that the compensatory role of duplicate genes is less important when the metabolite has a high connectivity, indicating that functional compensation by alternative pathways is common in the case of high connectivity. In conclusion, recently duplicated genes play an important role in the compensation of metabolic products only when the number of alternative pathways is small.
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