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

Area of Science:

• Microbiology
• Genomics
• Epigenetics

Background:

• Phosphorothioation (PT) is a unique microbial DNA backbone modification involving sulfur insertion.
• PT regulates gene expression and host defense mechanisms in prokaryotes.
• The dnd and ssp gene families are known to be involved in PT synthesis.

Purpose of the Study:

• To investigate the distribution and diversity of PT genes within the human gut microbiome.
• To identify novel PT synthesis systems and their genomic context.
• To characterize PT dinucleotide settings and their genomic localization.

Main Methods:

• Analysis of 13,663 human gut microbiome genomes for dnd, ssp, and brx genes.
• Genetic validation of type 4 BREX brx genes in Bacteroides salyersiae.
• Mass spectrometric analysis and PT-specific DNA sequencing of 226 gut microbiome isolates.

Main Results:

• 6.3% of analyzed genomes contained dnd or ssp genes, primarily in Bacillota, Bacteroidota, and Pseudomonadota.
• Novel PT synthesis systems, including type 4 BREX brx genes, were identified and validated.
• Eight PT dinucleotide settings were confirmed, with enrichment in rRNA genes and depletion at gene boundaries.

Conclusions:

• The human gut microbiome is a rich source for discovering novel prokaryotic epigenetic modifications like PT.
• PT synthesis systems are widely distributed in gut microbes, particularly the oxidation-sensitive variants.
• PT exhibits specific genomic preferences, suggesting functional roles in gene regulation and defense.