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

Proc Natl Acad Sci U S A. 2022 Oct 4;119(40):e2207332119. doi: 10.1073/pnas.2207332119. Epub 2022 Sep 26.

Abstract

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.

Keywords: DNA damage; Paf1 complex; RNA polymerase II removal; Rad26; Spt4/Spt5 complex.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Cycle Proteins / metabolism
  • Cullin Proteins* / metabolism
  • DNA Damage*
  • Elongin* / genetics
  • Elongin* / metabolism
  • Nuclear Proteins* / genetics
  • Nuclear Proteins* / metabolism
  • Proteasome Endopeptidase Complex / metabolism
  • RNA Polymerase II* / metabolism
  • Saccharomyces cerevisiae Proteins* / metabolism
  • Saccharomyces cerevisiae* / metabolism
  • Transcription Factors / metabolism
  • Transcriptional Elongation Factors / metabolism

Substances

  • CTR9 protein, S cerevisiae
  • Cell Cycle Proteins
  • Cullin Proteins
  • Elongin
  • Nuclear Proteins
  • PAF1 protein, S cerevisiae
  • Saccharomyces cerevisiae Proteins
  • Transcription Factors
  • Transcriptional Elongation Factors
  • RNA Polymerase II
  • Proteasome Endopeptidase Complex
  • RAD26 protein, S cerevisiae