Crystal Structure of the Core Module of the Yeast Paf1 Complex

Chen, Feilong; Liu, Beibei; Zeng, Jianwei; Guo, Lu; Ge, Xuan; Feng, Wei; Li, Defeng; Zhou, Hao; Long, Jiafu

doi:10.1016/j.jmb.2021.167369

Cited by 8 publications

(14 citation statements)

References 61 publications

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“…This observation, together with the findings showing that Ctr9 is a key scaffold protein for yeast PAF1C assembly and functional regulation ( 49 . 51 ), suggested that deletion of the Ctr9 subunit may result in disruption of intact PAF1C assembly and thus lead to defects in Rpb1 degradation in the ctr9Δ strain. The mechanisms by which the loss of the PAF1 , LEO1 , or CDC73 gene in yeast causes defects in DNA damage–induced Rpb1 degradation need to be further explored (for a detailed study, see Figs.…”

Section: Resultsmentioning

confidence: 99%

“…To test the role of the heterodimer Paf1/Leo1 in Elongin-Cullin complex–mediated Rpb1 ubiquitination in vitro, we first purified the yeast Paf1 (116-445) /Leo1 complex (deletion of the N-terminal Ctr9-binding region in Paf1 does not affect the interaction between Paf1 and Leo1 ( 47 , 51 ) and is beneficial for the expression and purification of the Paf1 (116-445) /Leo1 complex) ( SI Appendix , Fig. S4 A and lane 1 in SI Appendix , Fig.…”

Section: Resultsmentioning

confidence: 99%

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The Paf1 complex is required for RNA polymerase II removal in response to DNA damage

Chen

Liu

Zhou

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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Rpb1, the largest subunit of RNA polymerase II (RNAPII), is rapidly polyubiquitinated and degraded in response to DNA damage; this process is considered to be a “mechanism of last resort’’ employed by cells. The underlying mechanism of this process remains elusive. Here, we uncovered a previously uncharacterized multistep pathway in which the polymerase-associated factor 1 (Paf1) complex (PAF1C, composed of the subunits Ctr9, Paf1, Leo1, Cdc73, and Rtf1) is involved in regulating the RNAPII pool by stimulating Elongin-Cullin E3 ligase complex-mediated Rpb1 polyubiquitination and subsequent degradation by the proteasome following DNA damage. Mechanistically, Spt5 is dephosphorylated following DNA damage, thereby weakening the interaction between the Rtf1 subunit and Spt5, which might be a key step in initiating Rpb1 degradation. Next, Rad26 is loaded onto stalled RNAPII to replace the Spt4/Spt5 complex in an RNAPII-dependent manner and, in turn, recruits more PAF1C to DNA lesions via the binding of Rad26 to the Leo1 subunit. Importantly, the PAF1C, assembled in a Ctr9-mediated manner, coordinates with Rad26 to localize the Elongin-Cullin complex on stalled RNAPII, thereby inducing RNAPII removal, in which the heterodimer Paf1/Leo1 and the subunit Cdc73 play important roles. Together, our results clearly revealed a new role of the intact PAF1C in regulating the RNAPII pool in response to DNA damage.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

The Paf1 complex is required for RNA polymerase II removal in response to DNA damage

Chen

Liu

Zhou

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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“…There are several possible mechanisms to explain why the leo‐1(gk1081) mutant exhibited less severe defects in germ cell development. Recently, crystal structure analysis revealed that the reconstituted PAF1C quaternary Ctr9/Paf1/Cdc73/RTf1 complex may act as the core module of the yeast PAF1C in the absence of the Leo1 subunit (Chen et al, 2022). The mutant LEO‐1( gk1081 ) protein was shown to have lost more than two‐thirds of the carboxyl‐terminal region (Kubota et al, 2014), which include the PAF1‐binding domain of the Homo sapiens LEO1 protein (Chu et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

The PAF1 complex cell autonomously promotes oogenesis in Caenorhabditis elegans

et al. 2022

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The RNA polymerase II-associated factor 1 complex (PAF1C) is a protein complex that consists of LEO1, RTF1, PAF1, CDC73, and CTR9, and has been shown to be involved in RNA polymerase II-mediated transcriptional and chromatin regulation. Although it has been shown to regulate a variety of biological processes, the precise role of the PAF1C during germ line development has not been clarified. In this study, we found that reduction in the function of the PAF1C components, LEO-1, RTFO-1, PAFO-1, CDC-73, and CTR-9, in Caenorhabditis elegans affects oogenesis. Defects in oogenesis were also confirmed using an oocyte maturation marker, OMA-1::GFP. While four to five OMA-1::GFP-positive oocytes were observed in wild-type animals, their numbers were significantly decreased in pafo-1 mutant and leo-1(RNAi), pafo-1(RNAi), and cdc-73(RNAi) animals. Expression of a functional PAFO-1::mCherry transgene in the germline significantly rescued the oogenesisdefective phenotype of the pafo-1 mutants, suggesting that expression of the PAF1C in germ cells is required for oogenesis. Notably, overexpression of OMA-1::GFP partially rescued the oogenesis defect in the pafo-1 mutants.Based on our findings, we propose that the PAF1C promotes oogenesis in a cell-autonomous manner by positively regulating the expression of genes involved in oocyte maturation.

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“…PAF1c is composed of subunits PAF1, CTR9, CDC73, LEO1, RTF1 and, in human cells, SKI8 ( Mueller and Jaehning, 2002 ). In higher eukaryotes, PAF1c is recruited to promoters and enhancers of active genes, where it directly binds to the CTD and outer surface of RNApol2, as well as to elongation factor SPT4/5 (DSIF) ( Yu et al, 2015 ; Chen et al, 2021 ).…”

Section: Paf1 Complexmentioning

confidence: 99%

“…PAF1c strongly associates with P-TEFb and both factors show interdependent recruitment to target gene promoters ( Yu et al, 2015 ). RNAi-mediated PAF1c depletion, depending on the cell line and specific study, resulted in either increased or decreased RNApol2 pausing ( Yu et al, 2015 ; Chen et al, 2021 ). In both cases, observed effects were linked to alterations in P-TEFb recruitment.…”

Section: Paf1 Complexmentioning

confidence: 99%

Transcription Pause and Escape in Neurodevelopmental Disorders

2022

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Transcription pause-release is an important, highly regulated step in the control of gene expression. Modulated by various factors, it enables signal integration and fine-tuning of transcriptional responses. Mutations in regulators of pause-release have been identified in a range of neurodevelopmental disorders that have several common features affecting multiple organ systems. This review summarizes current knowledge on this novel subclass of disorders, including an overview of clinical features, mechanistic details, and insight into the relevant neurodevelopmental processes.

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Crystal Structure of the Core Module of the Yeast Paf1 Complex

Cited by 8 publications

References 61 publications

The Paf1 complex is required for RNA polymerase II removal in response to DNA damage

The Paf1 complex is required for RNA polymerase II removal in response to DNA damage

The PAF1 complex cell autonomously promotes oogenesis in Caenorhabditis elegans

Transcription Pause and Escape in Neurodevelopmental Disorders

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