Structural insights into nuclear transcription by eukaryotic DNA-dependent RNA polymerases

Girbig, Mathias; Misiaszek, Agata D.; Müller, Christoph W.

doi:10.1038/s41580-022-00476-9

Cited by 69 publications

(58 citation statements)

References 243 publications

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“…Ribosome biogenesis is a complex and metabolically costly process involving the activities of three cellular RNA polymerases, their RNA products, and hundreds of proteins [ 1 , 2 , 3 , 4 , 5 ]. As protein synthesis is required for cell growth and survival, actively dividing cells produce 1–2 million ribosomes per cell cycle [ 2 ].…”

Section: Introduction: Rna Polymerase I Is An Essential Enzyme For Ri...mentioning

confidence: 99%

“…Over the next few decades, the structures and functions of three mammalian polymerases (Pol I, Pol II, and Pol III) were identified. Pol I synthesizes most rRNA, Pol II synthesizes mRNA and other non-coding and regulatory RNAs, whereas Pol III synthesizes tRNA and 5S rRNA [ 3 , 14 , 15 , 16 ]. Ribosome biogenesis thus requires the cooperation of all three RNA polymerases.…”

Section: Introduction: Rna Polymerase I Is An Essential Enzyme For Ri...mentioning

confidence: 99%

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Regulation of RNA Polymerase I Stability and Function

Pitts

Laiho

2022

Cancers

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RNA polymerase I is a highly processive enzyme with fast initiation and elongation rates. The structure of Pol I, with its in-built RNA cleavage ability and incorporation of subunits homologous to transcription factors, enables it to quickly and efficiently synthesize the enormous amount of rRNA required for ribosome biogenesis. Each step of Pol I transcription is carefully controlled. However, cancers have highjacked these control points to switch the enzyme, and its transcription, on permanently. While this provides an exceptional benefit to cancer cells, it also creates a potential cancer therapeutic vulnerability. We review the current research on the regulation of Pol I transcription, and we discuss chemical biology efforts to develop new targeted agents against this process. Lastly, we highlight challenges that have arisen from the introduction of agents with promiscuous mechanisms of action and provide examples of agents with specificity and selectivity against Pol I.

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Section: Introduction: Rna Polymerase I Is An Essential Enzyme For Ri...mentioning

confidence: 99%

Section: Introduction: Rna Polymerase I Is An Essential Enzyme For Ri...mentioning

confidence: 99%

Regulation of RNA Polymerase I Stability and Function

Pitts

Laiho

2022

Cancers

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“…Coupling between the swiveling motion and trigger loop folding was also observed in cryo-EM studies of cyanobacterial RNAP transcription complexes (manuscript in preparation), suggesting that it is a universally conserved feature of transcription in bacteria. Since domains and motifs of RNAPs are highly conserved in all cellular RNAPs including bacterial, archaeal and three nuclear eukaryotic RNAPs (RNAPI, RNAPII and RNAPIII) (46–48), the coupling between swiveling and trigger loop folding may occur in all organisms.…”

Section: Discussionmentioning

confidence: 99%

“…Since domains and motifs of RNAPs are highly conserved in all cellular RNAPs including bacterial, archaeal and three nuclear eukaryotic RNAPs (RNAPI, RNAPII and RNAPIII) (46)(47)(48), the coupling between swiveling and trigger loop folding may occur in all organisms.…”

Section: The Mechanism Of Nusg-dependent Transcription Pausingmentioning

confidence: 99%

Allosteric mechanism of transcription inhibition by NusG-dependent pausing of RNA polymerase

Vishwakarma

Qayyum

Babitzke

et al. 2022

Preprint

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NusG is a general transcription elongation factor that stimulates transcription pausing in Gram+ bacteria including Bacillus subtilis by sequence-specific interaction with a conserved pause-inducing -11TTNTTT-6 motif found in the non-template DNA (ntDNA) strand within the transcription bubble. To reveal the structural basis of NusG-dependent pausing, we determined the cryo-electron microscopy (cryo-EM) structure of a paused transcription complex containing RNAP, NusG, and the TTNTTT motif in the ntDNA strand. The interaction of NusG with the ntDNA strand expands the transcription bubble by positioning three consecutive T residues in a cleft between NusG and the β subunit lobe domain (β-lobe) of RNAP. We revealed that the RNAP swivel module rotation (swiveling), which widens (swiveled state) and narrows (non-swiveled state) a cleft between NusG and the β-lobe, is an intrinsic motion of RNAP and is directly linked to nucleotide binding at the active site and to trigger loop folding, an essential conformational change of all cellular RNAPs for the RNA synthesis reaction. We also determined cryo-EM structures of RNAP escaping from a paused transcription complex. These structures revealed the NusG-dependent pausing mechanism by which NusG-ntDNA interaction inhibits the transition from swiveled to non-swiveled states, thereby preventing trigger loop folding and RNA synthesis allosterically. This motion is also inhibited by formation of an RNA hairpin within the RNA exit channel. Thus, the pause half-life can be modulated by the strength of the NusG-ntDNA interaction and/or the stability of the RNA hairpin. NusG residues that interact with the TTNTTT motif are widely conserved in bacteria, suggesting that NusG-dependent pausing of transcription is widespread.

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“…Eukaryotic RNA polymerases (Pols I, II, and III) [ 1 ] are structurally homologous [ 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 ] but each Pol has unique genetic targets and they each play a distinct role in ribosome biogenesis [ 10 , 11 ]. Pol I transcription of the ribosomal DNA (rDNA) is tightly regulated and proportional to cellular growth rate [ 12 , 13 ].…”

Section: Introductionmentioning

confidence: 99%

RNA Polymerase I Is Uniquely Vulnerable to the Small-Molecule Inhibitor BMH-21

Jacobs

Fuller

Cooper

et al. 2022

Cancers

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Cancer cells require robust ribosome biogenesis to maintain rapid cell growth during tumorigenesis. Because RNA polymerase I (Pol I) transcription of the ribosomal DNA (rDNA) is the first and rate-limiting step of ribosome biogenesis, it has emerged as a promising anti-cancer target. Over the last decade, novel cancer therapeutics targeting Pol I have progressed to clinical trials. BMH-21 is a first-in-class small molecule that inhibits Pol I transcription and represses cancer cell growth. Several recent studies have uncovered key mechanisms by which BMH-21 inhibits ribosome biosynthesis but the selectivity of BMH-21 for Pol I has not been directly measured. Here, we quantify the effects of BMH-21 on Pol I, RNA polymerase II (Pol II), and RNA polymerase III (Pol III) in vitro using purified components. We found that BMH-21 directly impairs nucleotide addition by Pol I, with no or modest effect on Pols II and III, respectively. Additionally, we found that BMH-21 does not affect the stability of any of the Pols’ elongation complexes. These data demonstrate that BMH-21 directly exploits unique vulnerabilities of Pol I.

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Structural insights into nuclear transcription by eukaryotic DNA-dependent RNA polymerases

Cited by 69 publications

References 243 publications

Regulation of RNA Polymerase I Stability and Function

Regulation of RNA Polymerase I Stability and Function

Allosteric mechanism of transcription inhibition by NusG-dependent pausing of RNA polymerase

RNA Polymerase I Is Uniquely Vulnerable to the Small-Molecule Inhibitor BMH-21

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