The unstructured linker arms of MutL enable GATC site incision beyond roadblocks during initiation of DNA mismatch repair

Nucleic Acids Res. 2019 Dec 16;47(22):11667-11680. doi: 10.1093/nar/gkz834.


DNA mismatch repair (MMR) maintains genome stability through repair of DNA replication errors. In Escherichia coli, initiation of MMR involves recognition of the mismatch by MutS, recruitment of MutL, activation of endonuclease MutH and DNA strand incision at a hemimethylated GATC site. Here, we studied the mechanism of communication that couples mismatch recognition to daughter strand incision. We investigated the effect of catalytically-deficient Cas9 as well as stalled RNA polymerase as roadblocks placed on DNA in between the mismatch and GATC site in ensemble and single molecule nanomanipulation incision assays. The MMR proteins were observed to incise GATC sites beyond a roadblock, albeit with reduced efficiency. This residual incision is completely abolished upon shortening the disordered linker regions of MutL. These results indicate that roadblock bypass can be fully attributed to the long, disordered linker regions in MutL and establish that communication during MMR initiation occurs along the DNA backbone.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Pair Mismatch / genetics
  • CRISPR-Associated Protein 9 / genetics
  • DNA Mismatch Repair / genetics*
  • DNA Repair Enzymes / metabolism
  • DNA, Bacterial / genetics*
  • DNA-Binding Proteins / metabolism
  • DNA-Directed RNA Polymerases / genetics
  • Deoxyribonucleases, Type II Site-Specific / metabolism*
  • Endodeoxyribonucleases / metabolism
  • Escherichia coli / genetics*
  • Escherichia coli Proteins / metabolism*
  • Genomic Instability / genetics
  • MutL Proteins / metabolism*
  • MutS DNA Mismatch-Binding Protein / metabolism


  • DNA, Bacterial
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • MutL protein, E coli
  • DNA-Directed RNA Polymerases
  • CRISPR-Associated Protein 9
  • Endodeoxyribonucleases
  • methyl-directed mismatch repair protein, E coli
  • Deoxyribonucleases, Type II Site-Specific
  • GATC-specific type II deoxyribonucleases
  • MutL Proteins
  • MutS DNA Mismatch-Binding Protein
  • MutS protein, E coli
  • DNA Repair Enzymes