Structure of the DP1-DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases

PLoS Biol. 2019 Jan 18;17(1):e3000122. doi: 10.1371/journal.pbio.3000122. eCollection 2019 Jan.

Abstract

PolD is an archaeal replicative DNA polymerase (DNAP) made of a proofreading exonuclease subunit (DP1) and a larger polymerase catalytic subunit (DP2). Recently, we reported the individual crystal structures of the DP1 and DP2 catalytic cores, thereby revealing that PolD is an atypical DNAP that has all functional properties of a replicative DNAP but with the catalytic core of an RNA polymerase (RNAP). We now report the DNA-bound cryo-electron microscopy (cryo-EM) structure of the heterodimeric DP1-DP2 PolD complex from Pyrococcus abyssi, revealing a unique DNA-binding site. Comparison of PolD and RNAPs extends their structural similarities and brings to light the minimal catalytic core shared by all cellular transcriptases. Finally, elucidating the structure of the PolD DP1-DP2 interface, which is conserved in all eukaryotic replicative DNAPs, clarifies their evolutionary relationships with PolD and sheds light on the domain acquisition and exchange mechanism that occurred during the evolution of the eukaryotic replisome.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence / genetics
  • Binding Sites / genetics
  • Catalytic Domain
  • Cryoelectron Microscopy / methods
  • DNA / genetics
  • DNA Replication / genetics
  • DNA-Binding Proteins / metabolism
  • DNA-Binding Proteins / ultrastructure*
  • DNA-Directed DNA Polymerase / metabolism
  • DNA-Directed DNA Polymerase / ultrastructure
  • DNA-Directed RNA Polymerases / metabolism
  • DNA-Directed RNA Polymerases / ultrastructure
  • Protein Domains / genetics
  • Protein Subunits / metabolism
  • Pyrococcus abyssi / metabolism
  • Pyrococcus abyssi / ultrastructure
  • Transcription Factor DP1 / metabolism
  • Transcription Factor DP1 / ultrastructure*
  • Transcription Factors / metabolism
  • Transcription Factors / ultrastructure*

Substances

  • DNA-Binding Proteins
  • Protein Subunits
  • TFDP2 protein, human
  • Transcription Factor DP1
  • Transcription Factors
  • DNA
  • DNA-Directed RNA Polymerases
  • DNA-Directed DNA Polymerase

Grant support

The fellowship of PR is funded by Sorbonnes University ED515 and Fondation pour la Recherche Médicale. The work is funded by an ANR JCJC grant ANR-17-CE11-0005-01, Institut Pasteur, Ifremer, and the Swedish Research Council (grant no. 2017-04641). The cryo-EM data were collected at the Swedish National Cryo-EM Facility funded by the Knut and Alice Wallenberg Foundation and the Science for Life Laboratory. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.