A unique methylation pattern by a type I HsdM methyltransferase prepares for DpnI rare cutting sites in the Pseudomonas aeruginosa PAO1 genome

FEMS Microbiol Lett. 2019 Mar 1;366(5):fnz053. doi: 10.1093/femsle/fnz053.


A physical genome map of Pseudomonas aeruginosa PAO1 had been constructed in the late 1980s by combinatorial SpeI/DpnI long-range restriction mapping. Whereas SpeI was known to cleave within the infrequent 5'-ACTAGT hexanucleotide, the rare recognition site 5'-Gm6ATC for the methylation-sensitive 4-cutter DpnI in the PAO1 genome remained elusive. Resequencing the PAO1 genome with the methylation-sensitive Single Molecule Real-Time (SMRT) sequencing technology identified DpnI to cleave the PAO1 genome at 15 palindromic GAC(N)6Gm6ATC(N)6GTC recognition sites with the central Gm6ATC palindrome to be methylated on both strands by the clone PAO1-specific type I HsdM superfamily methyltransferase M.PaePAOI (PA2735).

Keywords: bacteriology; genome reconstruction; methylation; restriction modification.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / metabolism*
  • DNA Methylation*
  • DNA Restriction-Modification Enzymes / metabolism*
  • DNA, Bacterial / genetics
  • DNA, Bacterial / metabolism
  • Deoxyribonucleases, Type II Site-Specific / metabolism*
  • Genome, Bacterial / genetics*
  • Pseudomonas aeruginosa / genetics*
  • Restriction Mapping
  • Sequence Analysis, DNA


  • Bacterial Proteins
  • DNA Restriction-Modification Enzymes
  • DNA, Bacterial
  • HsdM protein, Bacteria
  • Deoxyribonucleases, Type II Site-Specific