Functional Genomics and Plant Molecular Imaging, Center for Protein Engineering, CIP, Department of Life Sciences, University of Liège, Liège, Belgium.
PLoS Genet. 2013;9(8):e1003707. doi: 10.1371/journal.pgen.1003707. Epub 2013 Aug 22.
Among the rare colonizers of heavy-metal rich toxic soils, Arabidopsis halleri is a compelling model extremophile, physiologically distinct from its sister species A. lyrata, and A. thaliana. Naturally selected metal hypertolerance and extraordinarily high leaf metal accumulation in A. halleri both require Heavy Metal ATPase4 (HMA4) encoding a PIB-type ATPase that pumps Zn(2+) and Cd(2+) out of specific cell types. Strongly enhanced HMA4 expression results from a combination of gene copy number expansion and cis-regulatory modifications, when compared to A. thaliana. These findings were based on a single accession of A. halleri. Few studies have addressed nucleotide sequence polymorphism at loci known to govern adaptations. We thus sequenced 13 DNA segments across the HMA4 genomic region of multiple A. halleri individuals from diverse habitats. Compared to control loci flanking the three tandem HMA4 gene copies, a gradual depletion of nucleotide sequence diversity and an excess of low-frequency polymorphisms are hallmarks of positive selection in HMA4 promoter regions, culminating at HMA4-3. The accompanying hard selective sweep is segmentally eclipsed as a consequence of recurrent ectopic gene conversion among HMA4 protein-coding sequences, resulting in their concerted evolution. Thus, HMA4 coding sequences exhibit a network-like genealogy and locally enhanced nucleotide sequence diversity within each copy, accompanied by lowered sequence divergence between paralogs in any given individual. Quantitative PCR corroborated that, across A. halleri, three genomic HMA4 copies generate overall 20- to 130-fold higher transcript levels than in A. thaliana. Together, our observations constitute an unexpectedly complex profile of polymorphism resulting from natural selection for increased gene product dosage. We propose that these findings are paradigmatic of a category of multi-copy genes from a broad range of organisms. Our results emphasize that enhanced gene product dosage, in addition to neo- and sub-functionalization, can account for the genomic maintenance of gene duplicates underlying environmental adaptation.
在富含重金属的有毒土壤的少数殖民者中，拟南芥 halleri 是一个引人注目的极端微生物模型，在生理上与它的姐妹种 A. lyrata 和 A. thaliana 不同。自然选择的金属超耐性和拟南芥 halleri 中异常高的叶片金属积累都需要 Heavy Metal ATPase4（HMA4）编码一种 PIB 型 ATPase，该酶将 Zn（2+）和 Cd（2+）泵出特定的细胞类型。与拟南芥相比，HMA4 表达的强烈增强是由于基因拷贝数扩展和顺式调控修饰的组合。这些发现基于拟南芥 halleri 的单个入口。很少有研究涉及到已知控制适应的基因座的核苷酸序列多态性。因此，我们对来自不同生境的多个拟南芥 halleri 个体的 HMA4 基因组区域的 13 个 DNA 片段进行了测序。与侧翼三个串联 HMA4 基因拷贝的对照基因座相比，HMA4 启动子区域核苷酸序列多样性逐渐减少，低频多态性过剩是 HMA4 正选择的标志，最终在 HMA4-3 达到顶峰。由于 HMA4 蛋白编码序列之间反复发生异位基因转换，导致伴随的硬选择清除在 HMA4 区域被部分遮蔽，从而导致它们的协同进化。因此，HMA4 编码序列表现出一种网络状的系统发育，并且在每个拷贝中都存在局部增强的核苷酸序列多样性，同时在任何给定个体中的同源基因之间的序列差异降低。定量 PCR 证实，在拟南芥 halleri 中，三个基因组 HMA4 拷贝的转录本水平比拟南芥高出 20 到 130 倍。总之，我们的观察结果构成了由于增加基因产物剂量而自然选择的多态性的异常复杂模式。我们提出，这些发现是来自广泛生物的多拷贝基因的一类的范例。我们的研究结果强调，除了新功能和亚功能化之外，增强的基因产物剂量还可以解释环境适应的基因重复的基因组维持。
