title: DNA phosphorothioation is widespread and quantized in bacterial genomes.
abstract: 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.
authors.affiliation: Department of Biological Engineering, Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Lianrong
authors.initials: L
authors.lastname: Wang
authors.forename: Shi
authors.initials: S
authors.lastname: Chen
authors.forename: Kevin L
authors.initials: KL
authors.lastname: Vergin
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Giovannoni
authors.forename: Simon W
authors.initials: SW
authors.lastname: Chan
authors.forename: Michael S
authors.initials: MS
authors.lastname: DeMott
authors.forename: Koli
authors.initials: K
authors.lastname: Taghizadeh
authors.forename: Otto X
authors.initials: OX
authors.lastname: Cordero
authors.forename: Michael
authors.initials: M
authors.lastname: Cutler
authors.forename: Sonia
authors.initials: S
authors.lastname: Timberlake
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Alm
authors.forename: Martin F
authors.initials: MF
authors.lastname: Polz
authors.forename: Jarone
authors.initials: J
authors.lastname: Pinhassi
authors.forename: Zixin
authors.initials: Z
authors.lastname: Deng
authors.forename: Peter C
authors.initials: PC
authors.lastname: Dedon
mesh_terms: D001483:Base Sequence; D002853:Chromatography, Liquid; D003001:Cloning, Molecular; D016000:Cluster Analysis; D019295:Computational Biology; D017931:DNA Primers / Q000235:genetics; D004269:DNA, Bacterial / Q000378:metabolism*; D022761:Gene Transfer, Horizontal / Q000235:genetics*; D005798:Genes, Bacterial / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics; D008969:Molecular Sequence Data; D054735:Phosphorothioate Oligonucleotides / Q000378:metabolism*; D010802:Phylogeny; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D013455:Sulfur / Q000378:metabolism; D053719:Tandem Mass Spectrometry; D014737:Vibrionaceae / Q000235:genetics*
chemical_list: D017931:DNA Primers; D004269:DNA, Bacterial; D054735:Phosphorothioate Oligonucleotides; D013455:Sulfur