RNA polymerase I structure and transcription regulation

Abstract

Transcription of ribosomal RNA by RNA polymerase (Pol) I initiates ribosome biogenesis and regulates eukaryotic cell growth. The crystal structure of Pol I from the yeast Saccharomyces cerevisiae at 2.8 Å resolution reveals all 14 subunits of the 590-kilodalton enzyme, and shows differences to Pol II. An ‘expander’ element occupies the DNA template site and stabilizes an expanded active centre cleft with an unwound bridge helix. A ‘connector’ element invades the cleft of an adjacent polymerase and stabilizes an inactive polymerase dimer. The connector and expander must detach during Pol I activation to enable transcription initiation and cleft contraction by convergent movement of the polymerase ‘core’ and ‘shelf’ modules. Conversion between an inactive expanded and an active contracted polymerase state may generally underlie transcription. Regulatory factors can modulate the core–shelf interface that includes a ‘composite’ active site for RNA chain initiation, elongation, proofreading and termination.

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Figure 1: Crystal structure of Pol I.
Figure 2: Structure of the two largest Pol I subunits.
Figure 3: Subunit A12.2 and the TFIIF-like subcomplex A49–A34.5.
Figure 4: Expanded cleft, expander and unwound bridge helix.
Figure 5: Composite active site and A12.2 hairpin.
Figure 6: Connector and Pol I dimerization.

Accession codes

Accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors of the Pol I crystal structure have been deposited with the Protein Data Bank under accession number 4C2M.

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Acknowledgements

We thank C. Kuhn, who obtained the first Pol I crystals. We thank C. Bäjen, S. Benkert, S. Geiger, S. Jennebach, T. Gubbey and K. Maier. We thank the crystallization facility (Conti Department) and the Jentsch Department of the Max-Planck-Institut for Biochemistry. Part of this work was performed at the European Synchrotron Radiation Facility at Grenoble, France, and at the Swiss Light Source at the Paul-Scherrer-Institut, Villigen, Switzerland. C.E. was supported by a PhD student fellowship of the Boehringer Ingelheim Fonds, the Elite Network Bavaria program ‘Protein Dynamics in Health and Disease’, and the Graduate Research Academy ‘RNA Biology’ of SFB960. S.S. was supported by a postdoctoral fellowship of the Alexander-von-Humboldt Foundation. P.C. was supported by the Deutsche Forschungsgemeinschaft (SFB646, TR5, GraKo1721, SFB960, CIPSM, NIM), an Advanced Grant of the European Research Council, the Jung-Stiftung, and the Vallee Foundation.

Author information

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Authors

Contributions

C.E. planned and carried out experiments and crystal structure determination. S.S. advised on experimental and crystallographic work. A.C.C. performed computational crystallographic analysis. D.K. contributed to computational crystallography and model building. P.C. designed and supervised research and prepared the manuscript, with contributions from all authors.

Corresponding author

Correspondence to Patrick Cramer.

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Competing interests

The authors declare no competing financial interests.

Extended data figures and tables

Extended Data Figure 1 Activity of purified Pol I in vitro.

a, Pol I is active in RNA extension and cleavage. Purified S. cerevisiae Pol I and Pol II can extend RNA in a DNA–RNA scaffold in the presence of nucleoside triphosphate substrates (NTPs). In the absence of nucleoside triphosphate substrates, Pol I cleaves RNA. Transcription assays were performed as described9 using the DNA–RNA scaffold shown. After running a 20% acrylamide UREA gel, RNA was detected by fluorescence. b, Dynamic light scattering is consistent with a concentration-dependent Pol I dimer–monomer equilibrium in solution. Note that the sample with the higher Pol I concentration shows an increased hydrodynamic radius and apparent (estimated) molecular mass for the predominant peak by mass that accounts for over 96%. The method cannot distinguish monomeric and dimeric species. Thus, the estimated molecular mass observed at 3.5 mg ml−1 Pol I concentration (769 kDa) arises from a mixture of monomers (590 kDa) and dimers (1,180 kDa). c, De novo RNA synthesis activity on tailed DNA template. Assays were performed as described47 using the DNA template shown. After running a 20% acrylamide UREA gel, de novo synthesized, radioactive RNA was detected by phosphoimaging.

Extended Data Figure 2 Structure-based alignment of A190 and Rpb1.

Invariant and conserved residues are highlighted in green and light green, respectively. Secondary structure elements are indicated above and below the alignment for A190 and Rpb1, respectively (cylinders, helices; arrows, strands). Residues that form different folds in Pol I or form Pol-II-specific folds are in green or red, respectively (compare Fig. 1c).

Extended Data Figure 3 Structure-based alignment of A135 and Rpb2.

Invariant and conserved residues are highlighted in green and light green, respectively. Secondary structure elements are indicated above and below the alignment for A135 and Rpb2, respectively (cylinders, helices; arrows, strands). Residues that form different folds in Pol I or form Pol-II-specific folds are in green or red, respectively (compare Fig. 1c).

Extended Data Figure 4 Detailed comparison of A190–A135 with Rpb1–Rpb2.

a, Comparison of A190 domain structures (top) that differ significantly from their corresponding Pol II regions (bottom). Labelling of corresponding secondary structure elements is as for Pol II (ref. 7). New or lacking secondary structure elements are labelled. New elements were named according to the preceding Pol II element with small letters added alphabetically for subsequent elements. b, Comparison of A135 domain structures (top) that differ significantly from their corresponding Pol II regions (bottom) as in Extended Data Fig. 3.

Extended Data Figure 5 Structure of the subassembly AC40–AC19–Rpb10–Rpb12.

a, Schematic of domain structures. AC40 and AC19 were aligned with homologous Pol II subunits Rpb3 and Rpb11, respectively. Organization and annotation as in Fig. 2a. b, Ribbon view from the ‘back’ of the enzyme7 (left, Pol I; right, Pol II). c, d, Structure-based alignments of AC40 and Rpb3 (c) and of AC19 and Rpb11 (d). Invariant and conserved residues are highlighted in green and light green, respectively. Secondary structure elements are indicated above and below the alignment for AC40 and Rpb3, respectively (cylinders, helices; arrows, strands). Residues that form different folds in Pol I or form Pol-II-specific folds are in green or red, respectively (compare Fig. 1c).

Extended Data Figure 6 A12.2 and A49–A34.5.

a, Subunit A12.2 amino acid sequence alignment. The sequence of yeast S. cerevisiae A12.2 (Sc) was aligned with that of the human subunit (Homo sapiens; Hs), and the N- and C-terminal domains were aligned with their counterparts in the Pol II subunit Rpb9 and the Pol II elongation factor TFIIS14, respectively. b, Interaction of A49–A34.5 with Pol I core domains. The view is from the front of the enzyme7 (Fig. 1). Different Pol I subunit domains are coloured as in Figs 2 and 3.

Extended Data Figure 7 Shift in domain positions between Pol I and Pol II.

Individual domain fragments of Pol I were isolated and superposed onto their counterparts in Pol II and subsequently recombined to form a ‘pseudo-Pol II’ model. This pseudo-Pol II model was then superposed onto the complete Pol I structure over a single common domain (indicated by column headings). The resulting root mean squared deviation (r.m.s.d.) Cα (Å) value for every individual domain (indicated by row headings) was calculated using PyMol and coloured according to value (green to yellow = 0.0 to 3.0 Å, orange = 3.0 to 4.0 Å, and red >4.0 Å).

Extended Data Figure 8 Structure and conservation of the connector and expander.

a, The connector binds the adjacent polymerase. The electron density is not continuous between the end of the A43 N-terminal part (residue Ile 250) and the beginning of the A43 connector in the adjacent polymerase. The connector cannot be assigned to A43 from the same polymerase because the observed distance between the last residue in the stalk and the first residue in the connector (>72 Å) cannot be spanned with only 12 residues. By contrast, the distance from Ile 250 to the connector in the cleft of the neighbouring polymerase is 18 Å and easily spanned by the missing residues. We note that dimeric forms of Pol I were previously observed in two-dimensional arrays59. b, Amino acid sequence alignment of the connector region in S. cerevisiae (Sc); Candida glabrata (Cg); Homo sapiens (Hs) and Mus musculus (Mm). Secondary structure elements are indicated above the alignment (K5 helix, cylinder; strands D1, D2; arrows). Residues that are involved in the interface with the Pol I clamp and cleft and showed a buried surface area in excess of 40 Å2 are indicated with an asterisk above the alignment. Buried surfaces were calculated with the PISA server60. A structure-based alignment of the A14–A43 stalk residues was published9,61 and is not included here. c, Amino acid sequence alignment of the expander region in S. cerevisiae, C. glabrata, H. sapiens and M. musculus. Secondary structure elements are indicated above the alignment (helices, cylinders; strands, arrows). Residues that are involved in the interface with the Pol I cleft and showed a buried surface area in excess of 40 Å2 are indicated with an asterisk above the alignment. Buried surfaces were calculated with the PISA server60. d, Previously obtained crosslinks11 of the expander element map to the Pol I cleft. Crosslinks to A190 and A135 are indicated in grey and wheat respectively.

Extended Data Table 1 RNA polymerase subunits in S. cerevisiae
Extended Data Table 2 Diffraction data and statistics

Supplementary information

Conformational differences between Pol I and Pol II illustrated by polymerase module movement

The video illustrates the differences in conformation between RNA polymerases I and II, and begins with a top view of Pol II. The core, shelf, clamp, stalk and lobe modules are coloured grey, magenta, orange, yellow and blue respectively. The structure morphs from a Pol II to Pol I conformation, highlighting their differences in cleft width. The Pol I specific subunits are then shown briefly before being faded out and the structure morphs back to the Pol II conformation. The video was generated using UCSF chimera. (MOV 13395 kb)

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Engel, C., Sainsbury, S., Cheung, A. et al. RNA polymerase I structure and transcription regulation. Nature 502, 650–655 (2013). https://doi.org/10.1038/nature12712

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