Genetic Organization, Length Conservation, and Evolution of RNA Polymerase II Carboxyl-Terminal Domain
Genetic Organization, Length Conservation, and Evolution of RNA Polymerase II Carboxyl-Terminal Domain
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DOI：
10.1093/molbev/msq151
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发表时间：
2010-11-01
影响因子：
10.7
通讯作者：
Greenleaf, Arno L.
中科院分区：
文献类型：
--
作者：
Liu, Pengda;Kenney, John M.;Greenleaf, Arno L.
真核RNA聚合酶II （RNAP II）羧基末端结构域（CTD）是一个简单的串联迭代序列，通过协调与转录和加工因子的多种顺序相互作用，充当mRNA合成的中心协调者。尽管研究兴趣浓厚，但关于CTD的功能和进化限制的许多关键问题仍未得到解答；例如，是什么选择了规范的七肽序列，它在生物体多样性中的串联阵列，以及给定物种内恒定的CTD长度，最后，序列相同的重复结构如何协调与修饰酶和结合伙伴同时和顺序的多样性，阶段依赖的相互作用？在这里，我们研究了58个RNAP II CTD的序列进化比较，这些RNAP II CTD来自不同的分类群，代表了所有六个主要的真核超群，并采用酵母CTD的综合进化遗传、生化和生物物理分析，以进一步阐明该重复序列如何组织以实现最佳的RNAP II功能。我们发现CTD是由跨二七肽的不可分割的独立功能单元组成的，不仅每个单元周围有灵活的构象，而且需要有弹性的整体结构。更值得注意的是，无论序列的特征如何，最佳的CTD功能总是在近似野生型CTD长度而不是功能单元数量上实现的。我们的综合观察结果使我们提出了一个更新的CTD工作模型，在这个模型中，功能和进化约束需要一个灵活的CTD构象，由CTD序列和串联寄存器决定，以适应CTD-蛋白质相互作用的多样性和特定的CTD长度，而不是功能单元的数量，以正确排序和组织全局CTD-蛋白质相互作用。这些特征在进化多样性中的保存模式对比较真核生物中RNAP II的功能具有重要意义，并且可以更清楚地指导目前研究不足的生物中CTD功能的具体研究。
With a simple tandem iterated sequence, the carboxyl terminal domain (CTD) of eukaryotic RNA polymerase II (RNAP II) serves as the central coordinator of mRNA synthesis by harmonizing a diversity of sequential interactions with transcription and processing factors. Despite intense research interest, many key questions regarding functional and evolutionary constraints on the CTD remain unanswered; for example, what selects for the canonical heptad sequence, its tandem array across organismal diversity, and constant CTD length within given species and finally and how a sequence-identical, repetitive structure can orchestrate a diversity of simultaneous and sequential, stage-dependent interactions with both modifying enzymes and binding partners? Here we examine comparative sequence evolution of 58 RNAP II CTDs from diverse taxa representing all six major eukaryotic supergroups and employ integrated evolutionary genetic, biochemical, and biophysical analyses of the yeast CTD to further clarify how this repetitive sequence must be organized for optimal RNAP II function. We find that the CTD is composed of indivisible and independent functional units that span diheptapeptides and not only a flexible conformation around each unit but also an elastic overall structure is required. More remarkably, optimal CTD function always is achieved at approximately wild-type CTD length rather than number of functional units, regardless of the characteristics of the sequence present. Our combined observations lead us to advance an updated CTD working model, in which functional, and therefore, evolutionary constraints require a flexible CTD conformation determined by the CTD sequence and tandem register to accommodate the diversity of CTD-protein interactions and a specific CTD length rather than number of functional units to correctly order and organize global CTD-protein interactions. Patterns of conservation of these features across evolutionary diversity have important implications for comparative RNAP II function in eukaryotes and can more clearly direct specific research on CTD function in currently understudied organisms.