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<p>Among dozens of microbial DNA modifications regulating gene expression and host defense, phosphorothioation (PT) is the only known backbone modification, with sulfur inserted at a non-bridging oxygen by <i>dnd</i> and <i>ssp</i> gene families. Here we explored the distribution of PT genes in 13,663 human gut microbiome genomes, finding that 6.3% possessed <i>dnd</i> or <i>ssp</i> genes predominantly in Bacillota, Bacteroidota, and Pseudomonadota. This analysis revealed several previously undescribed PT synthesis systems, including type 4 Bacteriophage Exclusion (BREX)&#xa0;type 4 <i>brx</i> genes, which we genetically validated in <i>Bacteroides salyersiae</i>. Mass spectrometric analysis of DNA from 226 gut microbiome isolates possessing <i>dnd</i>, <i>ssp</i>, and <i>brx</i> genes revealed 8 PT dinucleotide settings confirmed in 10 consensus sequences by PT-specific DNA sequencing. Genomic analysis showed PT enrichment in rRNA genes and depletion at gene boundaries. These results illustrate the power of the microbiome for discovering prokaryotic epigenetics and the widespread distribution of oxidation-sensitive PTs in gut microbes.</p>

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Phosphorothioate DNA modification by BREX type 4 systems in the human gut microbiome

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年1月22日

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  • Yifeng Yuan,
  • Michael S. DeMott,
  • Shane R. Byrne,
  • Katia Flores,
  • Mathilde Poyet,
  • Mathieu Groussin,
  • Brittany Berdy,
  • John Rusine Bahunde,
  • Catherine Girard,
  • Jenni Lehtimäki,
  • Audax Z. P. Mabulla,
  • Ivan Emil Mwikarago,
  • Yvonne Ayerki Nartey,
  • Le Thanh Tu Nguyen,
  • Charles A. Onyekwere,
  • Lewis R. Roberts,
  • B. Jesse Shapiro,
  • Tommi Vatanen,
  • Laurie E. Comstock,
  • Eric J. Alm,
  • Peter C. Dedon

摘要

Among dozens of microbial DNA modifications regulating gene expression and host defense, phosphorothioation (PT) is the only known backbone modification, with sulfur inserted at a non-bridging oxygen by dnd and ssp gene families. Here we explored the distribution of PT genes in 13,663 human gut microbiome genomes, finding that 6.3% possessed dnd or ssp genes predominantly in Bacillota, Bacteroidota, and Pseudomonadota. This analysis revealed several previously undescribed PT synthesis systems, including type 4 Bacteriophage Exclusion (BREX) type 4 brx genes, which we genetically validated in Bacteroides salyersiae. Mass spectrometric analysis of DNA from 226 gut microbiome isolates possessing dnd, ssp, and brx genes revealed 8 PT dinucleotide settings confirmed in 10 consensus sequences by PT-specific DNA sequencing. Genomic analysis showed PT enrichment in rRNA genes and depletion at gene boundaries. These results illustrate the power of the microbiome for discovering prokaryotic epigenetics and the widespread distribution of oxidation-sensitive PTs in gut microbes.