TADB 3.0: an updated database of bacterial toxin-antitoxin loci and associated mobile genetic elements

Abstract

TADB 3.0 (https://bioinfo-mml.sjtu.edu.cn/TADB3/) is an updated database that provides comprehensive information on bacterial types I to VIII toxin-antitoxin (TA) loci. Compared with the previous version, three major improvements are introduced: First, with the aid of text mining and manual curation, it records the details of 536 TA loci with experimental support, including 102, 403, 8, 14, 1, 1, 3 and 4 TA loci of types I to VIII, respectively; Second, by leveraging the upgraded TA prediction tool TAfinder 2.0 with a stringent strategy, TADB 3.0 collects 211 697 putative types I to VIII TA loci predicted in 34 789 completely sequenced prokaryotic genomes, providing researchers with a large-scale dataset for further follow-up analysis and characterization; Third, based on their genomic locations, relationships of 69 019 TA loci and 60 898 mobile genetic elements (MGEs) are visualized by interactive networks accessible through the user-friendly web page. With the recent updates, TADB 3.0 may provide improved in silico support for comprehending the biological roles of TA pairs in prokaryotes and their functional associations with MGEs.

Graphical Abstract

Figure 1.

Updated web interface of TADB 3.0. (A) The functional modules of TADB 3.0 on the home page. (B) The ‘Browse’ web page displaying information on the relBE family TA locus (VCA0503/VC_RS15830-VCA0504/VC_RS15835) in Vibrio cholerae O1 biovar El Tor str. N16961. (C) An overview of the features of TA locus VCA0503-VCA0504 on the detailed information page. (D) Visualization of the genomic context of TA locus by SVGene. (E) Protein domains of the toxin VCA0503 and the antitoxin VCA0504 predicted by InterProScan. (F) Interactive networks highlighting the MGEs associated with the VCA0503-VCA0504 TA locus identified by VRprofile2. Similar MGEs were defined as MGEs with pairwise Mash distances lower than 0.01. (G) Visualization of the gene structures around the TA-associated MGEs by SVGene using an IS element flanked by TA locus VCA0503-VCA0504 as an example. (H) Partial view of the comparison of similar MGEs by clinker and clustermap.js.

Figure 2.

Relationships of the TADB-archived TA loci and MGEs of the prokaryotic organisms. TA-associated MGEs are defined as the MGEs harboring TA loci or the ISs/transposons flanked by TA loci with an interval <5 kb in this study. The stacked bar plots display the proportion of TA-MGE relationships of each TA type. If one TA locus was associated with multiple MGEs or one MGE was associated with multiple TA loci, the relationships were calculated separately. The number of TA-MGE relationships, the number of TA loci associated with MGEs and the total number of TA loci were listed on the right side of the bar plot.