DNA phosphorothioation is widespread and quantized in bacterial genomes

Proc Natl Acad Sci U S A. 2011 Feb 15;108(7):2963-8. doi: 10.1073/pnas.1017261108. Epub 2011 Feb 1.


Phosphorothioate (PT) modification of DNA, with sulfur replacing a nonbridging phosphate oxygen, was recently discovered as a product of the dnd genes found in bacteria and archaea. Given our limited understanding of the biological function of PT modifications, including sequence context, genomic frequencies, and relationships to the diversity of dnd gene clusters, we undertook a quantitative study of PT modifications in prokaryotic genomes using a liquid chromatography-coupled tandem quadrupole mass spectrometry approach. The results revealed a diversity of unique PT sequence contexts and three discrete genomic frequencies in a wide range of bacteria. Metagenomic analyses of PT modifications revealed unique ecological distributions, and a phylogenetic comparison of dnd genes and PT sequence contexts strongly supports the horizontal transfer of dnd genes. These results are consistent with the involvement of PT modifications in a type of restriction-modification system with wide distribution in prokaryotes.

Publication types

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

MeSH terms

  • Base Sequence
  • Chromatography, Liquid
  • Cloning, Molecular
  • Cluster Analysis
  • Computational Biology
  • DNA Primers / genetics
  • DNA, Bacterial / metabolism*
  • Gene Transfer, Horizontal / genetics*
  • Genes, Bacterial / genetics*
  • Genome, Bacterial / genetics*
  • Genomics
  • Molecular Sequence Data
  • Phosphorothioate Oligonucleotides / metabolism*
  • Phylogeny*
  • Reverse Transcriptase Polymerase Chain Reaction
  • Sequence Analysis, DNA
  • Sulfur / metabolism
  • Tandem Mass Spectrometry
  • Vibrionaceae / genetics*


  • DNA Primers
  • DNA, Bacterial
  • Phosphorothioate Oligonucleotides
  • Sulfur