The roles of whole-genome and small-scale duplications in the functional specialization of Saccharomyces cerevisiae genes.
The roles of whole-genome and small-scale duplications in the functional specialization of Saccharomyces cerevisiae genes.
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DOI：
10.1371/journal.pgen.1003176
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发表时间：
2013
期刊：
影响因子：
4.5
通讯作者：
Jones GW
中科院分区：
文献类型：
--
作者：
Fares MA;Keane OM;Toft C;Carretero-Paulet L;Jones GW
长期以来，研究人员一直痴迷于基因复制可以产生新功能的想法，认为这一过程具有巨大的进化重要性。经验数据表明，全基因组复制(WGD)比小规模复制(SSD)更有可能被保留，尽管它们对复制的功能命运的相对贡献尚不清楚。利用遗传互作图谱和对进化了2,200代的27个酿酒酵母基因组的重新测序，我们发现SSD-复制导致了新的功能化，而WGD-复制导致了祖先功能的分割。这一结论得到以下结论的支持：(A)SSD-副本比独体和WGD-副本建立了更多的遗传互作；(B)SSD-副本比WGD-副本共享更多的交互伙伴；(C)WGD-副本的相互作用伙伴在功能上比SSD-副本更相关；(D)SSD-副本的基因副本之间在功能上的差异更大，同时保持了更多的重叠功能，并且在亚细胞位置上的差异比WGD-副本的差异更大；以及(E)SSD-副本比WGD-副本在更大程度上补充了它们的功能。我们提出了一个新的模型，揭示了基因复制后进化的复杂性。基因复制涉及一个基因的加倍，产生一个相同的基因拷贝。早期的进化理论预测，当一个基因拷贝执行祖先功能时，另一个基因拷贝在没有强烈选择限制的情况下，可以进化到探索替代功能。由于基因复制具有产生新功能的潜力，因此具有生物复杂性，因此被认为具有巨大的进化重要性。复制基因获得新功能的方式仍然是密集研究的重点。复制的机制--小基因组区域的复制与基因组复制--会影响复制的命运吗？虽然已经证明复制的机制决定了基因在复制中的持久性，但描述由全基因组或小规模复制产生的复制的功能命运的模型仍然很难理解。在这里，我们表明，尽管在酿酒酵母中有大量的遗传物质来源于全基因组复制，但这些复制专门用于祖先功能的子集。相反，小规模的复制品产生了新的功能。我们描述并测试了一个模型来解释由不同机制产生的重复序列的进化动力学。我们的结果揭示了复制的功能命运和复制机制在产生功能多样性中的作用。
Researchers have long been enthralled with the idea that gene duplication can generate novel functions, crediting this process with great evolutionary importance. Empirical data shows that whole-genome duplications (WGDs) are more likely to be retained than small-scale duplications (SSDs), though their relative contribution to the functional fate of duplicates remains unexplored. Using the map of genetic interactions and the re-sequencing of 27 Saccharomyces cerevisiae genomes evolving for 2,200 generations we show that SSD-duplicates lead to neo-functionalization while WGD-duplicates partition ancestral functions. This conclusion is supported by: (a) SSD-duplicates establish more genetic interactions than singletons and WGD-duplicates; (b) SSD-duplicates copies share more interaction-partners than WGD-duplicates copies; (c) WGD-duplicates interaction partners are more functionally related than SSD-duplicates partners; (d) SSD-duplicates gene copies are more functionally divergent from one another, while keeping more overlapping functions, and diverge in their sub-cellular locations more than WGD-duplicates copies; and (e) SSD-duplicates complement their functions to a greater extent than WGD–duplicates. We propose a novel model that uncovers the complexity of evolution after gene duplication. Gene duplication involves the doubling of a gene, originating an identical gene copy. Early evolutionary theory predicted that, as one gene copy is performing the ancestral function, the other gene copy, devoid from strong selection constraints, could evolve exploring alternative functions. Because of its potential to generate novel functions, hence biological complexity, gene duplication has been credited with enormous evolutionary importance. The way in which duplicated genes acquire novel functions remains the focus of intense research. Does the mechanism of duplication—duplication of small genome regions versus genome duplication—influence the fate of duplicates? Although it has been shown that the mechanism of duplication determines the persistence of genes in duplicate, a model describing the functional fates of duplicates generated by whole-genome or small-scale duplications remains largely obscure. Here we show that despite the large amount of genetic material originated by whole-genome duplication in the yeast Saccharomyces cerevisiae, these duplicates specialized in subsets of ancestral functions. Conversely, small-scale duplicates originated novel functions. We describe and test a model to explain the evolutionary dynamics of duplicates originated by different mechanisms. Our results shed light on the functional fates of duplicates and role of the duplication mechanism in generating functional diversity.
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