Identification of Three Type II Toxin-Antitoxin Systems in Model Bacterial Plant Pathogen Dickeya dadantii 3937

Abstract

Type II toxin-antitoxin (TA) systems are genetic elements usually encoding two proteins: a stable toxin and an antitoxin, which binds the toxin and neutralizes its toxic effect. The disturbance in the intracellular toxin and antitoxin ratio typically leads to inhibition of bacterial growth or bacterial cell death. Despite the fact that TA modules are widespread in bacteria and archaea, the biological role of these systems is ambiguous. Nevertheless, a number of studies suggests that the TA modules are engaged in such important processes as biofilm formation, stress response or virulence and maintenance of mobile genetic elements. The Dickeya dadantii 3937 strain serves as a model for pathogens causing the soft-rot disease in a wide range of angiosperm plants. Until now, several chromosome-encoded type II TA systems were identified in silico in the genome of this economically important bacterium, however so far only one of them was experimentally validated. In this study, we investigated three putative type II TA systems in D. dadantii 3937: ccdAB2Dda, phd-docDda and dhiTA, which represents a novel toxin/antitoxin superfamily. We provide an experimental proof for their functionality in vivo both in D. dadantii and Escherichia coli. Finally, we examined the prevalence of those systems across the Pectobacteriaceae family by a phylogenetic analysis.

Systematic transcriptome analysis allows the identification of new type I and type II Toxin/Antitoxin systems located in the superintegron of Vibrio cholerae

“…Proteins were identical in all, but one strains (NCTC 8457). In addition to D. dadantii [42], this TA family was also found (with at least 85% coverage and at least 50% identity) in several other marine bacteria: other Vibrios, Halomonas, Shewanella, Nitrincola, Rheinheimera, Marinomonas, Photobacterium, Edwardsiella. Acquisition through horizontal transfer among these marine species is thus likely at the origin of this large distribution.…”

“…During our work, a new toxin also exhibiting a DUF4160 domain was recently identified in Dickeya dadantii, a plant pathogen bacteria, also found in fresh waters [42]. Protein comparison showed that VCA0497 has 64% identity with the newly identified DhiT toxin, while VCA0498 exhibits 59% homology with its associated DhiA antitoxin.…”

“…So, VCA0497 toxin neutralization occurs by both occlusion of its active site by the antitoxin and by expression decreases, as described in type II TA systems [33e35]. VCA0497 contains a DUF4160 domain, as the recently identified type II TA system DhiT toxin in D. dadantii [42] and has 64% identity with it. Moreover, VCA0498 exhibits 59% homology with its associated DhiA antitoxin.…”

A novel double-ribonuclease toxin-antitoxin system linked to the stress response and survival of Acidovorax citrulli

“…oryzicola ( 35 ), Hok-Sok in Erwinia amylovora ( 36 ), EcnA-EcnB in Xanthomonas citri subsp. citri ( 37 ), CcdA-CcdB, Phd-Doc and DhiT-DhiA in Dickeya dadantii ( 38 ), and MazE-MazF in Agrobacterium tumefaciens ( 39 ).…”