dndDB: a database focused on phosphorothioation of the DNA backbone

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• The Dnd DNA degradation phenotype, linked to the dnd gene cluster, is found in diverse bacteria.
• This cluster mediates DNA phosphorothioate modification, incorporating sulfur into the DNA backbone.
• Identified dnd clusters are predominantly located on mobile genetic elements like genomic islands.

Purpose of the Study:

• To create a comprehensive database (dndDB) of DNA phosphorothioation (Dnd) phenomenon data.
• To organize experimental and bioinformatics data on dnd genes, phenotypes, and associated genomic elements.
• To provide accessible tools for researching dnd genes and their functions.

Main Methods:

• Compiled data from scientific literature and in silico analyses.
• Integrated information on Dnd phenotype, dnd gene clusters, genomic islands, and Dnd proteins.
• Included similarity search, sequence alignment, and phylogenetic tools for data exploration.

Main Results:

• dndDB contains data from 24 bacterial species with the Dnd phenotype.
• Identified 26 syntenic dnd clusters, 25 dnd-bearing genomic islands, and 1 dnd plasmid.
• Annotated 114 dnd genes and 397 related genes within the database.

Conclusions:

• dndDB facilitates efficient investigation of dnd DNA modification and island-encoded functions.
• The database supports research into the roles of dnd genes in host organisms.
• dndDB version 1.0 is publicly accessible for research use.