Evolution of DNA replication origin specification and gene silencing mechanisms

Nat Commun. 2020 Oct 14;11(1):5175. doi: 10.1038/s41467-020-18964-x.


DNA replication in eukaryotic cells initiates from replication origins that bind the Origin Recognition Complex (ORC). Origin establishment requires well-defined DNA sequence motifs in Saccharomyces cerevisiae and some other budding yeasts, but most eukaryotes lack sequence-specific origins. A 3.9 Å structure of S. cerevisiae ORC-Cdc6-Cdt1-Mcm2-7 (OCCM) bound to origin DNA revealed that a loop within Orc2 inserts into a DNA minor groove and an α-helix within Orc4 inserts into a DNA major groove. Using a massively parallel origin selection assay coupled with a custom mutual-information-based modeling approach, and a separate analysis of whole-genome replication profiling, here we show that the Orc4 α-helix contributes to the DNA sequence-specificity of origins in S. cerevisiae and Orc4 α-helix mutations change genome-wide origin firing patterns. The DNA sequence specificity of replication origins, mediated by the Orc4 α-helix, has co-evolved with the gain of ORC-Sir4-mediated gene silencing and the loss of RNA interference.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA Replication
  • DNA, Fungal / genetics
  • Evolution, Molecular
  • Gene Expression Regulation, Fungal*
  • Gene Silencing*
  • Mutation
  • Origin Recognition Complex / metabolism*
  • Origin Recognition Complex / ultrastructure
  • Protein Conformation, alpha-Helical / genetics
  • Replication Origin / genetics*
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Saccharomyces cerevisiae Proteins / ultrastructure
  • Silent Information Regulator Proteins, Saccharomyces cerevisiae / metabolism
  • Substrate Specificity / genetics


  • DNA, Fungal
  • ORC2 protein, S cerevisiae
  • ORC4 protein, S cerevisiae
  • Origin Recognition Complex
  • SIR4 protein, S cerevisiae
  • Saccharomyces cerevisiae Proteins
  • Silent Information Regulator Proteins, Saccharomyces cerevisiae