Structural basis of RNA polymerase III transcription repression by Maf1

ABSTRACTMaf1 is a highly conserved central regulator of transcription by RNA polymerase III (Pol III), and Maf1 activity influences a wide range of phenotypes from metabolic efficiency to lifespan. Here, we present a 3.3 Å cryo-EM structure of yeast Maf1 bound to Pol III, which establishes how Maf1 achieves transcription repression. In the Maf1-bound state, Pol III elements that are involved in transcription initiation are sequestered, and the active site is sealed off due to ordering of the mobile C34 winged helix 2 domain. Specifically, the Maf1 binding site overlaps with the binding site of the Pol III transcription factor TFIIIB and DNA in the pre-initiation complex, rationalizing that binding of Maf1 and TFIIIB to Pol III are mutually exclusive. We validate our structure using variants of Maf1 with impaired transcription-inhibition activity. These results reveal the exact mechanism of Pol III inhibition by Maf1, and rationalize previous biochemical data.

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Structural basis of RNA polymerase III transcription initiation

Nature ◽

10.1038/nature25441 ◽

2018 ◽

Vol 553 (7688) ◽

pp. 301-306 ◽

Cited By ~ 55

Author(s):

Guillermo Abascal-Palacios ◽

Ewan Phillip Ramsay ◽

Fabienne Beuron ◽

Edward Morris ◽

Alessandro Vannini

Keyword(s):

Rna Polymerase ◽

Transcription Initiation ◽

Rna Polymerase Iii ◽

Structural Basis ◽

Polymerase Iii

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Novel layers of RNA polymerase III control affecting tRNA gene transcription in eukaryotes

Open Biology ◽

10.1098/rsob.170001 ◽

2017 ◽

Vol 7 (2) ◽

pp. 170001 ◽

Cited By ~ 18

Author(s):

Ewa Leśniewska ◽

Magdalena Boguta

Keyword(s):

Transcription Factors ◽

Rna Polymerase ◽

Transcription Initiation ◽

Rna Polymerase Iii ◽

Negative Regulator ◽

Promoter Regions ◽

Polymerase Iii ◽

Short Transcript ◽

Nucleotide Resolution ◽

Pol Iii

RNA polymerase III (Pol III) transcribes a limited set of short genes in eukaryotes producing abundant small RNAs, mostly tRNA. The originally defined yeast Pol III transcriptome appears to be expanding owing to the application of new methods. Also, several factors required for assembly and nuclear import of Pol III complex have been identified recently. Models of Pol III based on cryo-electron microscopy reconstructions of distinct Pol III conformations reveal unique features distinguishing Pol III from other polymerases. Novel concepts concerning Pol III functioning involve recruitment of general Pol III-specific transcription factors and distinctive mechanisms of transcription initiation, elongation and termination. Despite the short length of Pol III transcription units, mapping of transcriptionally active Pol III with nucleotide resolution has revealed strikingly uneven polymerase distribution along all genes. This may be related, at least in part, to the transcription factors bound at the internal promoter regions. Pol III uses also a specific negative regulator, Maf1, which binds to polymerase under stress conditions; however, a subset of Pol III genes is not controlled by Maf1. Among other RNA polymerases, Pol III machinery represents unique features related to a short transcript length and high transcription efficiency.

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Transcription factor TFIIIB and transcription by RNA polymerase III

Biochemical Society Transactions ◽

10.1042/bst0341082 ◽

2006 ◽

Vol 34 (6) ◽

pp. 1082-1087 ◽

Cited By ~ 35

Author(s):

G.A. Kassavetis ◽

E.P. Geiduschek

Keyword(s):

Rna Polymerase ◽

Transcription Initiation ◽

Transcriptional Start Site ◽

Rna Polymerase Iii ◽

Initiation Factor ◽

Regulation Of Transcription ◽

Start Site ◽

High Mobility Group Protein ◽

Polymerase Iii ◽

Pol Iii

pol (RNA polymerase) III is charged with the task of transcribing nuclear genes encoding diverse small structural and catalytic RNAs. We present a brief review of the current understanding of several aspects of the pol III transcription apparatus. The focus is on yeast and, more specifically, on Saccharomyces cerevisiae; preponderant attention is given to the TFs (transcription initiation factors) and especially to TFIIIB, which is the core pol III initiation factor by virtue of its role in recruiting pol III to the transcriptional start site and its essential roles in forming the transcription-ready open promoter complex. Certain relatively recent developments are also selected for brief comment: (i) the genome-wide analysis of occupancy of pol III-transcribed genes (and other loci) by the transcription apparatus and the location of pol III transcription in the cell; (ii) progress toward a mechanistic and molecular understanding of the regulation of transcription by pol III in yeast; and (iii) recent experiments identifying a high mobility group protein as a fidelity factor that assures selection of the precise transcriptional start site at certain pol III promoters.

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Structural basis for RNA polymerase III transcription repression by Maf1

Nature Structural & Molecular Biology ◽

10.1038/s41594-020-0383-y ◽

2020 ◽

Vol 27 (3) ◽

pp. 229-232 ◽

Cited By ~ 3

Author(s):

Matthias K. Vorländer ◽

Florence Baudin ◽

Robyn D. Moir ◽

René Wetzel ◽

Wim J. H. Hagen ◽

...

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Iii ◽

Structural Basis ◽

Transcription Repression ◽

Polymerase Iii

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Faculty Opinions recommendation of Structural basis of RNA polymerase III transcription initiation.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.732522926.793581677 ◽

2021 ◽

Author(s):

Benoit Coulombe

Keyword(s):

Rna Polymerase ◽

Transcription Initiation ◽

Rna Polymerase Iii ◽

Structural Basis ◽

Polymerase Iii

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A Region of Bdp1 Necessary for Transcription Initiation That Is Located within the RNA Polymerase III Active Site Cleft

Molecular and Cellular Biology ◽

10.1128/mcb.00263-15 ◽

2015 ◽

Vol 35 (16) ◽

pp. 2831-2840 ◽

Cited By ~ 11

Author(s):

Hui-Lan Hu ◽

Chih-Chien Wu ◽

Jin-Cheng Lee ◽

Hung-Ta Chen

Keyword(s):

Transcription Factor ◽

Rna Polymerase ◽

Active Site ◽

Transcription Initiation ◽

Rna Polymerase Iii ◽

Terminal Region ◽

Preinitiation Complex ◽

Polymerase Iii ◽

Active Site Cleft ◽

Pol Iii

The RNA polymerase III (Pol III)-specific transcription factor Bdp1 is crucial to Pol III recruitment and promoter opening in transcription initiation, yet structural information is sparse. To examine its protein-binding targets within the preinitiation complex at the residue level, photoreactive amino acids were introduced intoSaccharomyces cerevisiaeBdp1. Mutations within the highly conserved SANT domain cross-linked to the transcription factor IIB (TFIIB)-related transcription factor Brf1, consistent with the findings of previous studies. In addition, we identified an essential N-terminal region that cross-linked with the Pol III catalytic subunit C128 as well as Brf1. Closer examination revealed that this region interacted with the C128 N-terminal region, the N-terminal half of Brf1, and the C-terminal domain of the C37 subunit, together positioning this region within the active site cleft of the preinitiation complex. With our functional data, our analyses identified an essential region of Bdp1 that is positioned within the active site cleft of Pol III and necessary for transcription initiation.

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