TADB 2.0: an updated database of bacterial type II toxin–antitoxin loci

Abstract

TADB2.0 (http://bioinfo-mml.sjtu.edu.cn/TADB2/) is an updated database that provides comprehensive information about bacterial type II toxin–antitoxin (TA) loci. Compared with the previous version, the database refined and the new data schema is employed. With the aid of text mining and manual curation, it recorded 6193 type II TA loci in 870 replicons of bacteria and archaea, including 105 experimentally validated TA loci. In addition, the newly developed tool TAfinder combines the homolog searches and the operon structure detection, allowing the prediction for type II TA pairs in bacterial genome sequences. It also helps to investigate the genomic context of predicted TA loci for putative virulence factors, antimicrobial resistance determinants and mobile genetic elements via alignments to the specific public databases. Additionally, the module TAfinder-Compare allows comparing the presence of the given TA loci across the close relative genomes. With the recent updates, TADB2.0 might provide better support for understanding the important roles of type II TA systems in the prokaryotic life activities.

A tripartite toxin‐antitoxin module induced by quorum sensing is associated with the persistence phenotype in Streptococcus mutans

“…Comparative genomics of 190 genomes of S. mutans strains revealed that SMU.166, SMU.167, and SMU.168 genes are highly conserved and present in all strains and thus, belong to the core‐genome of S. mutans species. Bioinformatics analysis of SMU.166/167/168 locus using the search engines TADB 2.0 and RASTA‐Bacteria for identifying TA loci in prokaryotes, predicted a putative type II toxin of 148 aa residues in length (predicted MW 16.9 kDa) encoded by SMU.167 gene with two possible partners, SMU.166 and SMU.168. The SMU.166 gene encodes a putative hypothetical protein of 171 aa residues and a theoretical MW of 19.4 kDa.…”

The RES domain toxins of RES‐Xre toxin‐antitoxin modules induce cell stasis by degrading NAD+

“…Homologs of the res-xre Pl locus are present in the genomes of many bacterial species and currently the TA database TADB 2.0 lists 115 of them (Xie et al, 2018). However, apart from the four highly conserved residues in the encoded toxins, alignment of selected RES toxin protein sequences shows that the proteins exhibit relatively low levels of sequence identity.…”

“…Type II TA modules are remarkably abundant in some prokaryotic genomes (Pandey and Gerdes, 2005;Jørgensen et al, 2009;Xie et al, 2018). For example, Mycobacterium tuberculosis strain H37Rv, a major human pathogen, encodes a stunning 88 putative TA modules (Ramage et al, 2009).…”

“…But overall, it is largely unknown why some prokaryotic genomes seem to 'attract' such a large number of TA modules. According to the TA database (TADB 2.0), most of the TA modules identified in the genome of P. luminescens belong to well-characterized TA families, such as RelBE, HigBA, ParDE, VapBC, MazEF, CcdAB and HicBA (Xie et al, 2018). However, a hitherto uncharacterized type II TA locus was also found, for which the putative toxin gene (plu2358) encodes a protein containing a so-called RES domain (Makarova et al, 2009).…”

A new sRNA‐mediated posttranscriptional regulation system for Bacillus subtilis

“…In types II, IV, V, and VI, the antitoxins are small proteins whereas in types I and III, the antitoxins are small regulatory RNAs (Lobato‐Marquez et al, ). The type II members are most abundant in bacteria and MazEF as a representative has been extensively studied (Coray, Wheeler, Heinemann, & Gardner, ; Lobato‐Marquez et al, ; Xie et al, ). The toxin MazF as an endoribonuclease cleaves single‐stranded RNA at the “ACA” recognition sequence whereas MazE is the cognate antitoxin for neutralization of MazF toxicity (Y. Zhang et al, ).…”