MutL sliding clamps coordinate exonuclease-independent Escherichia coli mismatch repair

Nat Commun. 2019 Nov 22;10(1):5294. doi: 10.1038/s41467-019-13191-5.

Abstract

A shared paradigm of mismatch repair (MMR) across biology depicts extensive exonuclease-driven strand-specific excision that begins at a distant single-stranded DNA (ssDNA) break and proceeds back past the mismatched nucleotides. Historical reconstitution studies concluded that Escherichia coli (Ec) MMR employed EcMutS, EcMutL, EcMutH, EcUvrD, EcSSB and one of four ssDNA exonucleases to accomplish excision. Recent single-molecule images demonstrated that EcMutS and EcMutL formed cascading sliding clamps on a mismatched DNA that together assisted EcMutH in introducing ssDNA breaks at distant newly replicated GATC sites. Here we visualize the complete strand-specific excision process and find that long-lived EcMutL sliding clamps capture EcUvrD helicase near the ssDNA break, significantly increasing its unwinding processivity. EcSSB modulates the EcMutL-EcUvrD unwinding dynamics, which is rarely accompanied by extensive ssDNA exonuclease digestion. Together these observations are consistent with an exonuclease-independent MMR strand excision mechanism that relies on EcMutL-EcUvrD helicase-driven displacement of ssDNA segments between adjacent EcMutH-GATC incisions.

Publication types

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

MeSH terms

  • DNA Breaks, Single-Stranded*
  • DNA Helicases / metabolism
  • DNA Helicases / physiology*
  • DNA Mismatch Repair / physiology*
  • DNA Repair / physiology
  • DNA Repair Enzymes / metabolism
  • DNA-Binding Proteins / metabolism
  • Endodeoxyribonucleases / metabolism
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Escherichia coli / physiology*
  • Escherichia coli Proteins / metabolism
  • Escherichia coli Proteins / physiology*
  • Microscopy, Fluorescence
  • MutL Proteins / metabolism
  • MutL Proteins / physiology*
  • Single Molecule Imaging

Substances

  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • MutL protein, E coli
  • SSB protein, E coli
  • Endodeoxyribonucleases
  • methyl-directed mismatch repair protein, E coli
  • UvrD protein, E coli
  • MutL Proteins
  • DNA Helicases
  • DNA Repair Enzymes