Structural mechanism of ATP-independent transcription initiation by RNA polymerase I

Yan Han; Chunli Yan; Thi Hoang Duong Nguyen; Ashleigh J. Jackobel; Ivaylo Ivanov; Bruce A. Knutson; Yuan He

doi:10.7554/eLife.27414

Structural mechanism of ATP-independent transcription initiation by RNA polymerase I

Yan Han, Chunli Yan, Thi Hoang Duong Nguyen, Ashleigh J. Jackobel, Ivaylo Ivanov, Bruce A. Knutson^*, Yuan He

^*Corresponding author for this work

Molecular Biosciences

Research output: Contribution to journal › Article › peer-review

51 Scopus citations

Abstract

Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a structure of Saccharomyces cerevisiae Pol I-CF-DNA to 3.8 Å resolution using single-particle cryo-electron microscopy. The structure reveals a bipartite architecture of Core Factor and its recognition of the promoter from 27 to 16. Core Factor’s intrinsic mobility correlates well with different conformational states of the Pol I cleft, in addition to the stabilization of either Rrn7 N-terminal domain near Pol I wall or the tandem winged helix domain of A49 at a partially overlapping location. Comparison of the three states in this study with the Pol II system suggests that a ratchet motion of the Core Factor-DNA sub-complex at upstream facilitates promoter melting in an ATP-independent manner, distinct from a DNA translocase actively threading the downstream DNA in the Pol II PIC.

Original language	English (US)
Article number	e27414
Journal	eLife
Volume	6
DOIs	https://doi.org/10.7554/eLife.27414
State	Published - Jun 17 2017

Funding

We thank Dr. Jonathan Remis, Dr. Valorie Bowman, and Dr. Thomas Klose for assistance with microscope operation and data collection, Dr. Frank DiMaio and Brandon Frenz for assistance for initial model building, and Jason Pattie for computer support. We are grateful to Dr. Ishwar Radhakrishnan, Susan Fishbain, and Ryan Abdella for helpful discussion and comments on the manuscript. We also thank the staff at the Structural Biology Facility (SBF) of Northwestern University and Cryo-EM Facility of Purdue University for technical support. This work was supported by a Cornew Innovation Award from the Chemistry of Life Processes Institute at Northwestern University (to Y He), a Catalyst Award by the Chicago Biomedical Consortium with support from the Searle Funds at The Chicago Community Trust (to Y He), an Institutional Research Grant from the American Cancer Society (IRG-15-173-21 to Y He), SUNY Research Foundation (to BAK), the Central New York Community Foundation (to BAK), the US National Institutes of Health (NCI5K22CA184235 to BAK, NIGMSGM110387 to II), the National Science Foundation (MCB-1149521 to II). Y Han is a recipient of the Chicago Biomedical Consortium Postdoctoral Research Grant. BAK is a Sinsheimer Scholar award from the Alexandrine and Alexander L Sinsheimer Fund. Computational resources were provided in part by XSEDE (CHE110042) and the National Energy Research for Scientific Computing Center (DE-AC02-05CH11231)., National Cancer Institute5K22CA184235 Bruce A Knutson, National Institute of General Medical SciencesGM110387 Ivaylo Ivanov, National Science FoundationMCB-1149521 Ivaylo Ivanov, Alexandrine and Alexander L. Sinsheimer Fund Sinsheimer Scholar award Bruce A Knutson

ASJC Scopus subject areas

General Immunology and Microbiology
General Biochemistry, Genetics and Molecular Biology
General Neuroscience

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10.7554/eLife.27414

Cite this

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title = "Structural mechanism of ATP-independent transcription initiation by RNA polymerase I",

abstract = "Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a structure of Saccharomyces cerevisiae Pol I-CF-DNA to 3.8 {\AA} resolution using single-particle cryo-electron microscopy. The structure reveals a bipartite architecture of Core Factor and its recognition of the promoter from 27 to 16. Core Factor{\textquoteright}s intrinsic mobility correlates well with different conformational states of the Pol I cleft, in addition to the stabilization of either Rrn7 N-terminal domain near Pol I wall or the tandem winged helix domain of A49 at a partially overlapping location. Comparison of the three states in this study with the Pol II system suggests that a ratchet motion of the Core Factor-DNA sub-complex at upstream facilitates promoter melting in an ATP-independent manner, distinct from a DNA translocase actively threading the downstream DNA in the Pol II PIC.",

author = "Yan Han and Chunli Yan and Nguyen, {Thi Hoang Duong} and Jackobel, {Ashleigh J.} and Ivaylo Ivanov and Knutson, {Bruce A.} and Yuan He",

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AU - Ivanov, Ivaylo

AU - Knutson, Bruce A.

AU - He, Yuan

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N2 - Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a structure of Saccharomyces cerevisiae Pol I-CF-DNA to 3.8 Å resolution using single-particle cryo-electron microscopy. The structure reveals a bipartite architecture of Core Factor and its recognition of the promoter from 27 to 16. Core Factor’s intrinsic mobility correlates well with different conformational states of the Pol I cleft, in addition to the stabilization of either Rrn7 N-terminal domain near Pol I wall or the tandem winged helix domain of A49 at a partially overlapping location. Comparison of the three states in this study with the Pol II system suggests that a ratchet motion of the Core Factor-DNA sub-complex at upstream facilitates promoter melting in an ATP-independent manner, distinct from a DNA translocase actively threading the downstream DNA in the Pol II PIC.

AB - Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a structure of Saccharomyces cerevisiae Pol I-CF-DNA to 3.8 Å resolution using single-particle cryo-electron microscopy. The structure reveals a bipartite architecture of Core Factor and its recognition of the promoter from 27 to 16. Core Factor’s intrinsic mobility correlates well with different conformational states of the Pol I cleft, in addition to the stabilization of either Rrn7 N-terminal domain near Pol I wall or the tandem winged helix domain of A49 at a partially overlapping location. Comparison of the three states in this study with the Pol II system suggests that a ratchet motion of the Core Factor-DNA sub-complex at upstream facilitates promoter melting in an ATP-independent manner, distinct from a DNA translocase actively threading the downstream DNA in the Pol II PIC.

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Structural mechanism of ATP-independent transcription initiation by RNA polymerase I

Abstract

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RNA Polymerase I Initial Transcribing Complex State 1

RNA polymerase I Initial Transcribing Complex State 3

RNA polymerase I Initial Transcribing Complex State 2

Cite this

Structural mechanism of ATP-independent transcription initiation by RNA polymerase I

Abstract

Funding

ASJC Scopus subject areas

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Datasets

RNA Polymerase I Initial Transcribing Complex State 1

RNA polymerase I Initial Transcribing Complex State 3

RNA polymerase I Initial Transcribing Complex State 2

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