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Updated: Jun 4, 2026
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A Novel Saturation Mutagenesis Approach: Single Step Characterization of Regulatory Protein Binding Sites in RNA Using Phosphorothioates
Published on: August 21, 2018
DNA phosphorothioation is widespread and quantized in bacterial genomes
Lianrong Wang1, Shi Chen, Kevin L Vergin
1Department of Biological Engineering, Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Summary
This study quantifies phosphorothioate (PT) DNA modifications in prokaryotes, revealing diverse contexts and frequencies. Findings suggest horizontal gene transfer of dnd genes and PT modifications in restriction-modification systems.
Area of Science:
- Microbiology
- Genomics
- Biochemistry
Background:
- Phosphorothioate (PT) DNA modification involves sulfur substitution in the phosphate backbone.
- PT modifications are produced by dnd genes in bacteria and archaea.
- Biological functions, sequence contexts, and genomic frequencies of PT modifications remain poorly understood.
Purpose of the Study:
- To quantitatively investigate PT modifications in prokaryotic genomes.
- To explore sequence contexts, genomic frequencies, and ecological distributions of PT modifications.
- To analyze the relationship between dnd gene diversity and PT modification patterns.
Main Methods:
- Liquid chromatography-coupled tandem quadrupole mass spectrometry (LC-MS/MS) was employed for quantitative analysis.
- Prokaryotic genomes were analyzed for PT modification patterns.
- Metagenomic analyses were performed to assess ecological distributions.
Main Results:
- A wide diversity of unique PT sequence contexts was identified across various bacteria.
- Three distinct genomic frequencies of PT modifications were observed.
- Metagenomic data revealed unique ecological distributions of PT modifications.
- Phylogenetic analysis supported horizontal gene transfer of dnd genes.
Conclusions:
- PT modifications exhibit diverse genomic contexts and frequencies in bacteria.
- Horizontal transfer of dnd genes is strongly supported by phylogenetic comparisons.
- Results indicate PT modifications are likely involved in widespread prokaryotic restriction-modification systems.
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