Structure and function of the initially transcribing RNA polymerase II-TFIIB complex
Structure and function of the initially transcribing RNA polymerase II-TFIIB complex
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DOI：
10.1038/nature11715
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发表时间：
2013-01-17
期刊：
影响因子：
64.8
通讯作者：
Cramer, Patrick
中科院分区：
文献类型：
--
作者：
Sainsbury, Sarah;Niesser, Juergen;Cramer, Patrick
一般转录因子（TF）IIB是RNA聚合酶（Pol）II启动所必需的，并与其B-阅读元件一起延伸到Pol II活性中心裂缝中。Pol II-TFIIB复合物的低分辨率结构（1，2）表明TFIIB如何在DNA募集中发挥作用，但它们缺乏核酸和一半的B-阅读器，使其他TFIIB功能（3，4）神秘莫测。在这里，我们报告晶体结构的Pol II-TFIIB复合物从酵母酿酒酵母在3.4埃分辨率和最初的转录复合物，另外包含的DNA模板和6个核苷酸的RNA产品。这些结构揭示了整个B-阅读器和蛋白质-核酸相互作用，并与功能数据一起导致对转录起始的更完整的理解。TFIIB部分关闭聚合酶裂缝以定位DNA并协助其打开。B-阅读器不能到达活性位点，但结合上游的DNA模板链，以帮助识别起始序列和定位转录起始位点。TFIIB重排活性位点残基，诱导催化金属离子B的结合，并刺激初始RNA合成变构。TFIIB然后防止出现的DNA-RNA杂交双链体倾斜，这将损害RNA合成。当RNA生长超过6个核苷酸时，它与DNA分离，并通过B-阅读器环引导到其出口通道。一旦RNA长到12-13个核苷酸，它就会与TFIIB发生冲突，引发TFIIB置换和延伸复合物的形成。类似的机制可能是所有细胞转录的基础，因为所有真核生物和古细菌RNA聚合酶都使用TFIIB样因子（5），细菌起始因子σ具有TFIIB样拓扑结构（1，2），并含有在位置、电荷和功能上类似于B-阅读器环的环区3.2（6-8）。因此，TFIIB及其对应物可以解释区分RNA和DNA聚合酶的两个基本性质：引物独立的链起始和产物与模板的分离。
The general transcription factor (TF) IIB is required for RNA polymerase (Pol) II initiation and extends with its B-reader element into the Pol II active centre cleft. Low-resolution structures of the Pol II-TFIIB complex(1,2) indicated how TFIIB functions in DNA recruitment, but they lacked nucleic acids and half of the B-reader, leaving other TFIIB functions(3,4) enigmatic. Here we report crystal structures of the Pol II-TFIIB complex from the yeast Saccharomyces cerevisiae at 3.4 angstrom resolution and of an initially transcribing complex that additionally contains the DNA template and a 6-nucleotide RNA product. The structures reveal the entire B-reader and protein-nucleic acid interactions, and together with functional data lead to a more complete understanding of transcription initiation. TFIIB partially closes the polymerase cleft to position DNA and assist in its opening. The B-reader does not reach the active site but binds the DNA template strand upstream to assist in the recognition of the initiator sequence and in positioning the transcription start site. TFIIB rearranges active-site residues, induces binding of the catalytic metal ion B, and stimulates initial RNA synthesis allosterically. TFIIB then prevents the emerging DNA-RNA hybrid duplex from tilting, which would impair RNA synthesis. When the RNA grows beyond 6 nucleotides, it is separated from DNA and is directed to its exit tunnel by the B-reader loop. Once the RNA grows to 12-13 nucleotides, it clashes with TFIIB, triggering TFIIB displacement and elongation complex formation. Similar mechanisms may underlie all cellular transcription because all eukaryotic and archaeal RNA polymerases use TFIIB-like factors(5), and the bacterial initiation factor sigma has TFIIB-like topology(1,2) and contains the loop region 3.2 that resembles the B-reader loop in location, charge and function(6-8). TFIIB and its counterparts may thus account for the two fundamental properties that distinguish RNA from DNA polymerases: primer-independent chain initiation and product separation from the template.