PXD059148

PXD059148 is an original dataset announced via ProteomeXchange.

Title	Phosphorothioate DNA modification by BREX Type 4 systems in the human gut microbiome
Description	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 uncovered several putative new PT synthesis systems, including Type 4 Bacteriophage Exclusion (BREX) brx genes, which were 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 6 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.
HostingRepository	PRIDE
AnnounceDate	2025-01-21
AnnouncementXML	Submission_2025-01-21_09:12:15.832.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yifeng Yuan
SpeciesList	scientific name: human gut metagenome; NCBI TaxID: 408170;
ModificationList	sulfur containing modified residue
Instrument	6490 Triple Quadrupole LC/MS

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-22 20:32:54	ID requested
⏵ 1	2025-01-21 09:12:16	announced

10.1101/2024.06.03.597175;

submitter keyword: LC-MSMS,Phosphorothioate, human gut microbiome

Peter C. Dedon
contact affiliation	Department of Biological Engineering, Massachusetts Institute of Techonology, 77 Massachusetts Avenue, 56-731 Cambridge, MA 02139, USA Tel: 617-253-8017
contact email	pcdedon@mit.edu
lab head
Yifeng Yuan
contact affiliation	Biological Scientist
contact email	yuanyifeng@ufl.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD059148
     1. Label: PRIDE project
     2. Name: Phosphorothioate DNA modification by BREX Type 4 systems in the human gut microbiome