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

Area of Science:

• Microbiology
• Epigenetics
• Genomics

Background:

• Phosphorothioation (PT) is a unique microbial DNA backbone modification involving sulfur insertion.
• The dnd and ssp gene families are known to mediate PT synthesis.
• Understanding PT distribution and function is crucial for microbial gene regulation and host defense.

Purpose of the Study:

• To investigate the prevalence and distribution of PT genes within the human gut microbiome.
• To identify novel PT synthesis systems and their genetic basis.
• To characterize the genomic locations and sequence contexts of PT modifications.

Main Methods:

• Genome-wide analysis of 13,663 human gut microbiome genomes for dnd, ssp, and brx genes.
• Genetic validation of putative new PT systems, including BREX genes.
• Mass spectrometry 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.
• Several putative new PT systems were identified, including Type 4 Bacteriophage Exclusion (BREX) brx genes.
• Eight PT dinucleotide settings were confirmed in gut microbes, with PT enriched in rRNA genes and depleted at gene boundaries.

Conclusions:

• The human gut microbiome harbors a diverse array of PT systems, including novel ones.
• PT modifications are widespread and exhibit specific genomic localization patterns in gut microbes.
• This study highlights the microbiome as a valuable resource for discovering prokaryotic epigenetics and oxidation-sensitive DNA modifications.