Beilstein Mark A, Renfrew Kyle B, Song Xiangyu, Shakirov Eugene V, Zanis Michael J, Shippen Dorothy E
School of Plant Sciences, University of Arizona Department of Biochemistry and Biophysics, Texas A&M University
Department of Biochemistry and Biophysics, Texas A&M University.
Mol Biol Evol. 2015 May;32(5):1329-41. doi: 10.1093/molbev/msv025. Epub 2015 Feb 19.
Gene duplication is a major driving force in genome evolution. Here, we explore the nature and origin of the POT1 gene duplication in Arabidopsis thaliana. Protection of Telomeres (POT1) is a conserved multifunctional protein that modulates telomerase activity and its engagement with telomeres. Arabidopsis thaliana encodes two divergent POT1 paralogs termed AtPOT1a and AtPOT1b. AtPOT1a positively regulates telomerase activity, whereas AtPOT1b is proposed to negatively regulate telomerase and promote chromosome end protection. Phylogenetic analysis uncovered two independent POT1 duplication events in the plant kingdom, including one at the base of Brassicaceae. Tests for positive selection implemented in PAML revealed that the Brassicaceae POT1a lineage experienced positive selection postduplication and identified three amino acid residues with signatures of positive selection. A sensitive and quantitative genetic complementation assay was developed to assess POT1a function in A. thaliana. The assay showed that AtPOT1a is functionally distinct from single-copy POT1 genes in other plants. Moreover, for two of the sites with a strong signature of positive selection, substitutions that swap the amino acids in AtPOT1a for residues found in AtPOT1b dramatically compromised AtPOT1a function in vivo. In vitro-binding studies demonstrated that all three sites under positive selection specifically enhance the AtPOT1a interaction with CTC1, a core component of the highly conserved CST (CTC1/STN1/TEN1) telomere protein complex. Our results reveal a molecular mechanism for the role of these positively selected sites in AtPOT1a. The data also provide an important empirical example to refine theories of duplicate gene retention, as the outcome of positive selection here appears to be reinforcement of an ancestral function, rather than neofunctionalization. We propose that this outcome may not be unusual when the duplicated protein is a component of a multisubunit complex whose function is in part specified by other members.
基因复制是基因组进化的主要驱动力。在此，我们探究了拟南芥中POT1基因复制的本质和起源。端粒保护蛋白（POT1）是一种保守的多功能蛋白，可调节端粒酶活性及其与端粒的结合。拟南芥编码两个不同的POT1旁系同源基因，分别称为AtPOT1a和AtPOT1b。AtPOT1a正向调节端粒酶活性，而AtPOT1b则被认为负向调节端粒酶并促进染色体末端保护。系统发育分析揭示了植物界中两个独立的POT1复制事件，其中一个发生在十字花科基部。在PAML中进行的正选择测试表明，十字花科POT1a谱系在复制后经历了正选择，并鉴定出三个具有正选择特征的氨基酸残基。我们开发了一种灵敏且定量的遗传互补测定法来评估AtPOT1a在拟南芥中的功能。该测定法表明，AtPOT1a在功能上与其他植物中的单拷贝POT1基因不同。此外，对于两个具有强烈正选择特征的位点，将AtPOT1a中的氨基酸替换为AtPOT1b中发现的残基的替代突变在体内显著损害了AtPOT1a的功能。体外结合研究表明，所有三个受到正选择的位点均特异性增强了AtPOT1a与CTC1的相互作用，CTC1是高度保守的CST（CTC1/STN1/TEN1）端粒蛋白复合体的核心成分。我们的结果揭示了这些正选择位点在AtPOT1a中发挥作用的分子机制。这些数据还提供了一个重要的实证例子来完善重复基因保留理论，因为此处正选择的结果似乎是对祖先功能的强化，而非新功能化。我们提出，当复制的蛋白质是多亚基复合体的一个组成部分，其功能部分由其他成员确定时，这种结果可能并不罕见。
