Pif1-family helicases cooperatively suppress widespread replication-fork arrest at tRNA genes

Nat Struct Mol Biol. 2017 Feb;24(2):162-170. doi: 10.1038/nsmb.3342. Epub 2016 Dec 19.

Abstract

Saccharomyces cerevisiae expresses two Pif1-family helicases-Pif1 and Rrm3-which have been reported to play distinct roles in numerous nuclear processes. Here, we systematically characterized the roles of Pif1 helicases in replisome progression and lagging-strand synthesis in S. cerevisiae. We demonstrate that either Pif1 or Rrm3 redundantly stimulates strand displacement by DNA polymerase δ during lagging-strand synthesis. By analyzing replisome mobility in pif1 and rrm3 mutants, we show that Rrm3, with a partially redundant contribution from Pif1, suppresses widespread terminal arrest of the replisome at tRNA genes. Although both head-on and codirectional collisions induce replication-fork arrest at tRNA genes, head-on collisions arrest a higher proportion of replisomes. In agreement with this observation, we found that head-on collisions between tRNA transcription and replication are under-represented in the S. cerevisiae genome. We demonstrate that tRNA-mediated arrest is R-loop independent and propose that replisome arrest and DNA damage are mechanistically separable.

MeSH terms

  • DNA
  • DNA Helicases / physiology*
  • DNA Replication*
  • G-Quadruplexes
  • Genes, Fungal
  • RNA, Fungal / genetics
  • RNA, Fungal / metabolism
  • RNA, Transfer / genetics*
  • RNA, Transfer / metabolism
  • Saccharomyces cerevisiae / enzymology*
  • Saccharomyces cerevisiae Proteins / physiology*
  • Transcription, Genetic

Substances

  • Okazaki fragments
  • RNA, Fungal
  • Saccharomyces cerevisiae Proteins
  • DNA
  • RNA, Transfer
  • PIF1 protein, S cerevisiae
  • Rrm3 protein, S cerevisiae
  • DNA Helicases