Polymerase manager protein UmuD directly regulates Escherichia coli DNA polymerase III α binding to ssDNA

Nucleic Acids Res. 2013 Oct;41(19):8959-68. doi: 10.1093/nar/gkt648. Epub 2013 Jul 30.

Abstract

Replication by Escherichia coli DNA polymerase III is disrupted on encountering DNA damage. Consequently, specialized Y-family DNA polymerases are used to bypass DNA damage. The protein UmuD is extensively involved in modulating cellular responses to DNA damage and may play a role in DNA polymerase exchange for damage tolerance. In the absence of DNA, UmuD interacts with the α subunit of DNA polymerase III at two distinct binding sites, one of which is adjacent to the single-stranded DNA-binding site of α. Here, we use single molecule DNA stretching experiments to demonstrate that UmuD specifically inhibits binding of α to ssDNA. We predict using molecular modeling that UmuD residues D91 and G92 are involved in this interaction and demonstrate that mutation of these residues disrupts the interaction. Our results suggest that competition between UmuD and ssDNA for α binding is a new mechanism for polymerase exchange.

Publication types

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

MeSH terms

  • Binding, Competitive
  • DNA Polymerase III / chemistry
  • DNA Polymerase III / metabolism*
  • DNA, Single-Stranded / metabolism*
  • DNA-Directed DNA Polymerase / chemistry
  • DNA-Directed DNA Polymerase / genetics
  • DNA-Directed DNA Polymerase / metabolism*
  • Escherichia coli Proteins / chemistry
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism*
  • Mutation

Substances

  • DNA, Single-Stranded
  • Escherichia coli Proteins
  • DNA polymerase III, alpha subunit
  • DNA Polymerase III
  • DNA-Directed DNA Polymerase
  • UmuD protein, E coli