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RNA polymerase II at initiation

RNA polymerase II (RNAPII) is the enzyme responsible for synthesis of all mRNA in higher cells. As the central component of the eukaryotic transcription machinery, RNAPII is the final target of regulatory pathways that are ultimately responsible for cellular development, differentiation, and metabolic control. Publication of the high-resolution structure of yeast RNAPII (1, 2) and of a transcribing RNAPII/DNA/RNA complex (3) identified key structural elements central to many of the enzyme's functions and suggested mechanisms for RNA chain elongation and translocation of the polymerase along DNA (2). Although a possible mechanism for interaction of RNAPII with promoter DNA was also proposed, absent from the x-ray structures were subunits Rpb4 and Rpb7, which form a dissociable complex in yeast and are required for initiation.

The problem posed for crystallization of the complete initiation-competent RNAPII by the presence of substoichiometric amounts of the Rpb4/Rpb7 complex has now been overcome, and reports by Armache et al. (4) and Bushnell and Kornberg (5) in this issue of PNAS describe the structure of RNAPII, including all 12 component subunits. The x-ray structures of the initiation-competent RNAPII are in agreement with each other and with a previously published 18-A resolution structure calculated by cryoelectron microscopy (cryo-EM) and image analysis of single RNAPII particles (6). Although the cryo-EM structure of the 12-subunit RNAPII was correct, the proposed mode of interaction between the Rpb4/Rpb7 heterodimer and the 10-subunit (core) RNAPII [based on fitting the x-ray structure of the Archaeal homolog of the eukaryoytic Rpb4/Rpb7 complex (7) to the EM reconstruction] was flawed. A correct fit of the Archaeal Rpb4/Rpb7 homolog to the x-ray structures of the complete RNAPII confirms the location of the Rpb4/Rpb7 heterodimer with respect to the core RNAPII and establishes that contact of the heterodimer with the core RNAPII is mediated by Rpb7. The …