Qian Wenfeng, Zhang Jianzhi
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA;
Genome Res. 2014 Aug;24(8):1356-62. doi: 10.1101/gr.172098.114. Epub 2014 Jun 5.
Gene duplication is widely believed to facilitate adaptation, but unambiguous evidence for this hypothesis has been found in only a small number of cases. Although gene duplication may increase the fitness of the involved organisms by doubling gene dosage or neofunctionalization, it may also result in a simple division of ancestral functions into daughter genes, which need not promote adaptation. Hence, the general validity of the adaptation by gene duplication hypothesis remains uncertain. Indeed, a genome-scale experiment found similar fitness effects of deleting pairs of duplicate genes and deleting individual singleton genes from the yeast genome, leading to the conclusion that duplication rarely results in adaptation. Here we contend that the above comparison is unfair because of a known duplication bias among genes with different fitness contributions. To rectify this problem, we compare homologous genes from the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. We discover that simultaneously deleting a duplicate gene pair in S. cerevisiae reduces fitness significantly more than deleting their singleton counterpart in S. pombe, revealing post-duplication adaptation. The duplicates-singleton difference in fitness effect is not attributable to a potential increase in gene dose after duplication, suggesting that the adaptation is owing to neofunctionalization, which we find to be explicable by acquisitions of binary protein-protein interactions rather than gene expression changes. These results provide genomic evidence for the role of gene duplication in organismal adaptation and are important for understanding the genetic mechanisms of evolutionary innovation.
基因复制被广泛认为有助于适应，但这一假说的确凿证据仅在少数案例中被发现。尽管基因复制可能通过使基因剂量加倍或新功能化来提高相关生物体的适应性，但它也可能导致祖先功能简单地划分为子代基因，而这不一定会促进适应性。因此，基因复制导致适应这一假说的普遍有效性仍不确定。事实上，一项全基因组规模的实验发现，从酵母基因组中删除成对的重复基因和删除单个单拷贝基因产生的适应性影响相似，从而得出复制很少导致适应的结论。在这里，我们认为上述比较是不公平的，因为具有不同适应性贡献的基因之间存在已知的复制偏差。为纠正这个问题，我们比较了出芽酵母酿酒酵母和裂殖酵母粟酒裂殖酵母的同源基因。我们发现，在酿酒酵母中同时删除一对重复基因比在粟酒裂殖酵母中删除它们的单拷贝对应基因对适应性的降低要显著得多，这揭示了复制后的适应性。重复基因和单拷贝基因在适应性影响上的差异并非归因于复制后基因剂量的潜在增加，这表明适应性是由于新功能化，我们发现这可以通过二元蛋白质 - 蛋白质相互作用的获得而非基因表达变化来解释。这些结果为基因复制在生物体适应中的作用提供了基因组证据，对于理解进化创新的遗传机制具有重要意义。
