Structure and mechanism of the RNA polymerase II transcription machinery

Abstract

Advances in structure determination of the bacterial and eukaryotic transcription machinery have led to a marked increase in the understanding of the mechanism of transcription. Models for the specific assembly of the RNA polymerase II transcription machinery at a promoter, conformational changes that occur during initiation of transcription, and the mechanism of initiation are discussed in light of recent developments.

Figure 1

The pathway of transcription initiation and reinitiation for RNA Pol II.

Figure 2

General transcription factor structures. (a) Structure of TBP (green) bound to TATA-DNA with B-form DNA (grey and red) modeled upstream and downstream of the TATA box,. (b) Structure model of the TBP-TFIIA-TFIIB-DNA complex. TBP (green) is shown from the top binding to the TFIIB core domain (TFIIBc, blue) and TFIIA (large subunit magenta, small subunit yellow). The zinc ribbon domain (shown as β strands with red Zn atom) connects to the B-finger domain is normally located in the PIC within the Pol II active site and is connected to the TFIIBc domain through a flexible linker. This model is a composite of the DNA-TBP-TFIIBc, DNA-TBP-TFIIA, and the TFIIB Zn ribbon NMR and crystal structures ,–,,. (c) EM structure of human TFIID with density due to anti-TBP antibody shown in yellow and the three TFIID lobes labeled A, B, and C. Figure 2c provided by E. Nogales.

Figure 3

The ten subunit yeast RNA Pol II structure and structure of the elongation complex. (a) top view of RNA Pol II with the DNA template strand (blue) non-template strand (green), RNA (red) and active site Mg (magenta). Figure adapted from (b) Side view of Pol II looking into the active site cleft– . Subunits are colored as follows: Rpb1, light red; Rpb2, light blue; Rpb12, light green; Rpb3, red; Rpb11, dark green; Rpb5, dark yellow; Rpb9, orange, active site Mg, magenta sphere. (c) details of the interactions between Pol II and the DNA-RNA hybrid in elongating Pol II. Figure from.

Figure 4

EM structure of the Pol II-Mediator complex. Mediator (dark blue) shown with head, middle, and tail domains. Pol II (gold) shown with modeled upstream and downstream DNA (orange). The dot represents the presumed beginning of the CTD. Figure from .

Figure 5

Summary of human general transcription factor protein-DNA crosslinks at a promoter. Top line represents promoter DNA with the position of functional elements indicated. Arrow represents the transcription start site. The bars below the line show the extent of protein-DNA crosslinking with the indicated general transcription factor using a crosslinker incorporated into the DNA backbone and crosslinked after treatment with Sarkosyl. Use of a larger major groove crosslinking reagent without detergent challenge has shown even more extensive crosslinks across the promoter region,.

Figure 6

The Pol II-TFIIB complex and a model for the structure of the PIC. (a). X-ray structure of the Pol II-TFIIB complex with the TFIIB N-terminal domain backbone (yellow), and the clamp, wall, dock and jaw/lobe domains shown in red, dark blue, purple, and orange. (b). Model for PIC structure based on the Pol II-TFIIB structure. Colors the same as in panel (a) with TBP (green), the N-terminal TFIIB core domain (TFIIBc; yellow), and DNA (red and blue).

Figure 7

EM structure of the Pol II-TFIIF complex. Pol II is shown as a brown surface with TFIIF density in blue. The orientation shown is similar to that of Figs 3b and 6. Also shown is a model for downstream double stranded DNA entering the active site cleft (blue and green helix). Figure provided by F. Asturias.