Introduction

TADB 3.0 is a comprehensive database that dedicated to unraveling the intricate relationship between bacterial Toxin-Antitoxin (TA) systems and Mobile Genetic Elements (MGEs). TADB 3.0 represents a significant improvement over previous versions, which offers three major enhancements: (i) manual curation of > 500 types I to VIII TA loci with experimental evidence and support; (ii) collection of the TAfinder 2.0-predicted TA loci in > 34,000 completely sequenced prokaryotic genomes; (iii) graphical representation of the relationships of the TA loci and MGEs. It will facilitate research on in silico prediction of TA systems and research on the interplay between TA systems and MGEs.

TA system dataset

  • TA system data update. The database now includes 204 newly identified TA systems and contains all types of TAs besides type II, resulting in a total of 309 TA systems, including 245 type II TA loci. The data accuracy and reliability have been enhanced through manual curation and verification processes.

  • Browse data. In Browse page, users can search for TA loci based on TA family, host species or related MGEs of interest. Click the TA ID to view detailed information of TA loci (Example). Users can also browse TA loci by species or by classification.

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    TA-MGE relationships

    TA systems are found to be passengers on almost all kinds of MGEs, which allow these systems to rapidly disseminate through bacterial communities by horizontal transfer. Moreover, TA systems are suggested to contribute to the maintenance of MGEs, ensuring their persistence in bacterial populations and contributing to the survival of bacteria under environmental stress.

  • TA-related MGEs. By utilizing VRprofile2 (Wang, et al. Nucleic Acids Research, 2022), we identify 20,957 MGEs in bacterial strains with experimentally validated and bioinformatically predicted TA loci. By screening TA loci locate inside or in the 5 kb flanking regions of MGEs, we identified 2,577 TA-MGE relationships between 1,821 MGEs and 2,100 TA loci. Moreover, among these TA-related MGEs, we identified 277 highly similar TA-related MGE pairs with pairwise Mash distance < 0.01

  • Visualize TA-MGE relationships. In Statistics page, the TA-MGE relations can be visualized by a network. Click on MGE circles to view detailed information for each MGE (Example).

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  • View related MGEs for each TA pair. In TA pair detailed information page (Example), the TA-related MGEs are displayed in a network. If similar MGEs are found for an MGE (pairwise Mash distance < 0.01), these MGEs are also displayed.

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  • View detailed information for each TA-related MGE. By clicking MGE circles in Statistics page, or click 'View' in 'Related MGEs' section, detailed information of an MGE can be visualized by a gene structure plot and a table (Example).

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    TAfinder 2.0

    By using the newly added experimentally validated TA loci data, TAfinder is now able to identify all types of TA system in annotated or unannotated bacterial genomes. The workflow of TAfinder2 are described below:

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    For the input section, three types of input are acceptable: a pair of protein or DNA sequences, an annotated genome in the GenBank format, and an unannotated genome sequence in the FASTA format. For an unannotated genome sequence input, Prodigal would be used for protein-coding sequence (CDS) identification before sequence extraction. In the preprocess section, the extracted sequences would be filtered by user-defined maximum length (500 a.a. by default) and minimum length (30 a.a. by default). In the homology search section, the protein sequences are input to BLASTp and HMMER3 to search for protein homologues, while the genome sequence is input to BLASTn to identify RNA toxins and antitoxins. The E-value (0.01 by default) for BLAST and HMMER3 as well as the identities (30% by default) for BLAST are set to filter out the results. In the TA pairing section, for the identification of types II to VII TA loci, the toxin hits and antitoxin hits should be located in the same strand, and the maximum intergenic distance (150 bp by default) is set for identifying the TA operon structure. For the identification of type I TA loci, the toxin gene and antitoxin RNA should be located on the opposite DNA strands, rather than forming an operon structure on the same strand. In addition, for the identification of type VIII TA loci, we took into consideration the two experimentally validated type VIII systems. One type VIII TA locus had both RNAs located on the same strand (Ming Li et al.), while the other locus had the two RNAs located on the opposite strands (Jee Soo Choi et al.). Consequently, we predicted these two distinct type VIII TA loci based on their respective characteristics.