TSPDB: A curated resource of tailspike proteins with potential applications in phage research

Abstract

Phages are ubiquitous viruses that drive bacterial evolution through infection and replication within host bacteria. Phage tailspike proteins (TSPs) are key components of phage tail structures, exhibiting polysaccharide depolymerase activity and host specificity. Despite their potential as novel antimicrobials, few TSPs have been fully characterized due to laborious detection techniques. To address this, we present TSPDB, a curated resource for rapid detection of TSPs in genomics and metagenomics sequence data. We mined public databases, obtaining 17,211 TSP sequences, which were filtered to exclude duplicates and partial sequences, resulting in 8,099 unique TSP sequences. TSPDB contains TSPs from over 400 bacterial genera, with significant diversity among them as revealed by the phylogenetic analysis. The top 13 genera represented were Gram-positive, with Bacillus, Streptococcus, and Clostridium being the most common. Of note, Phage TSPs in Gram-positive bacteria were on average 1 Kbp larger than those in Gram-negative bacteria. TSPDB has been applied in a recent study to screen phage genomes, demonstrating its potential for functional annotation. TSPDB serves as a comprehensive repository and a resource for researchers in phage biology, particularly in phage associated therapy and antimicrobial or biocontrol applications. TSPDB is compatible with bioinformatics tools for in silico detection of TSPs in genomics and metagenomic data, and is freely accessible on GitHub and Figshare, providing a valuable resource for the scientific community.